Alignments for a candidate for gcvP in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvP in Echinicola vietnamensis KMM 6221, DSM 17526

Align Glycine dehydrogenase (decarboxylating), mitochondrial; Glycine cleavage system P protein; Glycine decarboxylase; Glycine dehydrogenase (aminomethyl-transferring); EC 1.4.4.2 (characterized)
to candidate Echvi_0744 Echvi_0744 glycine dehydrogenase (decarboxylating)

Query= SwissProt::P26969
         (1057 letters)



>FitnessBrowser__Cola:Echvi_0744
          Length = 966

 Score = 1129 bits (2919), Expect = 0.0
 Identities = 561/970 (57%), Positives = 710/970 (73%), Gaps = 18/970 (1%)

Query: 92   LKPSDTFPRRHNSATPDEQTKMAESVGFDTLDSLVDATVPKSIRLKEMKFNKFDGGLTEG 151
            L PS  F  RHN  + ++ ++M   +G  ++D L+D T+PK+I+L +          +E 
Sbjct: 5    LTPSVKFEDRHNGPSANDVSEMLSKIGASSIDELIDQTIPKAIQLDQPL--NLPEAKSEA 62

Query: 152  QMIEHMKDLASKNKVFKSFIGMGYYNTHVPPVILRNIMENPAWYTQYTPYQAEISQGRLE 211
              ++  + +A+KNK++KSFIG+GYY+T  P VILRN++ENP WYT YTPYQAEI+QGRLE
Sbjct: 63   AFLKDFRKMAAKNKIYKSFIGLGYYDTITPGVILRNVLENPGWYTAYTPYQAEIAQGRLE 122

Query: 212  SLLNFQTMITDLTGLPMSNASLLDEGTAAAEAMSMCNNIQKGKKKT---FIIASNCHPQT 268
            +L+NFQTM+ DLTG+ ++NASLLDEGTAAAEAM+M    +   KK    F +      QT
Sbjct: 123  ALVNFQTMVMDLTGMELANASLLDEGTAAAEAMNMLFATRPRDKKKATKFFVDEKVFIQT 182

Query: 269  IDICQTRADGFELKVVVKDLKDIDYKSGDVCGVLVQYPGTEGEVLDYGEFIKKAHANEVK 328
             +I +TRA    + +V   L +++ +  ++ GVL+QYP  EGE +DY   ++KA  + V 
Sbjct: 183  KEILKTRALPIGVTLVEGSLNELNLEDPELYGVLLQYPNAEGEAIDYKALVEKAKQHNVT 242

Query: 329  VVMASDLLALTVLKPPGEFGADIVVGSAQRFGVPMGYGGPHAAFLATSQEYKRMMPGRII 388
               ++DLLALT+L PPGE GAD+VVG+ QRFGVPMG+GGPHAA+ AT   YKR +PGRII
Sbjct: 243  TAFSADLLALTLLTPPGEMGADVVVGTTQRFGVPMGFGGPHAAYFATKDAYKRQVPGRII 302

Query: 389  GVSVDSSGKQALRMAMQTREQHIRRDKATSNICTAQALLANMAAMYAVYHGPEGLKAIAQ 448
            G+SVD  G +A RMA+QTREQHI+R++ATSNICTAQ LLA MA MYAVYHGP+GLK IA 
Sbjct: 303  GISVDKDGNKAYRMALQTREQHIKRERATSNICTAQVLLAVMAGMYAVYHGPKGLKDIAL 362

Query: 449  RVHGLAGVFALGLKKLGLEVQDLGFFDTVKVKTSNAKA--IADAAIKSEINLRVVDGNTI 506
            ++HGLA + A GL KLG E ++  +FDT+K+K  + K   I   A+  E+N R   G  +
Sbjct: 363  KIHGLAKLTAQGLAKLGFEQENEHYFDTLKIKVDDVKQSKIKAFALSHEMNFRYEPGY-V 421

Query: 507  TAAFDETTTLEDVDKLFKVFAGGKPVSFTA---ASLAPEFQNAIPSGLVRESPYLTHPIF 563
              AFDE  T+EDV ++ +VFA     S      AS+       +  GL R S Y+ H IF
Sbjct: 422  YLAFDEAKTMEDVQEIIEVFARTTHSSADVVDLASMVDHLSFEVSDGLRRTSDYMDHMIF 481

Query: 564  NTYQTEHELLRYIHRLQSKDLSLCHSMIPLGSCTMKLNATTEMMPVTWPSFTDLHPFAPT 623
            N + +EHE+LRYI RL+++DLSL HSMI LGSCTMKLNAT EM+PVTWP F  LHPF P 
Sbjct: 482  NAFHSEHEMLRYIKRLENRDLSLVHSMISLGSCTMKLNATAEMIPVTWPEFGQLHPFVPQ 541

Query: 624  EQAQGYQEMFNNLGDLLCTITGFDSFSLQPNAGAAGEYAGLMVIRAYHLSRGDHHRNVCI 683
            +QA GY  +F +L + L  ITGF   SLQPN+GA GE+AGLMVIRAYH SRG+ HRN+ +
Sbjct: 542  DQAAGYYALFQDLRNWLSEITGFAETSLQPNSGAQGEFAGLMVIRAYHESRGESHRNIAL 601

Query: 684  IPASAHGTNPASAAMVGMKIVTIGTDAKGNINIEELKKAAEKHKDNLSAFMVTYPSTHGV 743
            IP+SAHGTNPASA M GMK+V +  D KGNI++ +LK+ AEKHK+NLS+F+VTYPSTHGV
Sbjct: 602  IPSSAHGTNPASAVMAGMKVVIVKCDDKGNIDLADLKEKAEKHKENLSSFLVTYPSTHGV 661

Query: 744  YEEGIDDICKIIHDNGGQVYMDGANMNAQVGLTSPGWIGADVCHLNLHKTFCIPHGGGGP 803
            +EE I ++C+I+H+NGGQVYMDGANMNAQVGLTSPG IGADVCHLNLHKTFCIPHGGGGP
Sbjct: 662  FEEAIREMCQIVHENGGQVYMDGANMNAQVGLTSPGVIGADVCHLNLHKTFCIPHGGGGP 721

Query: 804  GMGPIGVKKHLAPFLPSHPVVPTGGIPAPENPQPLGSISAAPWGSALILPISYTYIAMMG 863
            GMGPI V KHL  FLPS P+V TGG       QP+ +ISAAP+GSA ILPISY YIAMMG
Sbjct: 722  GMGPICVAKHLEEFLPSSPLVKTGG------QQPISAISAAPFGSASILPISYAYIAMMG 775

Query: 864  SQGLTDASKIAILNANYMAKRLESYYPVLFRGVNGTVAHEFIIDLRGFKNTAGIEPEDVA 923
             +GL  A++ AILNANY+  RL  ++P L+ G  G  AHE I+D R FK   G+E ED+A
Sbjct: 776  REGLKHATQTAILNANYIKARLGEFFPTLYTGAQGRAAHEMIVDFREFK-AVGVEVEDIA 834

Query: 924  KRLMDYGFHGPTMSWPVAGTLMIEPTESESKAELDRFCDALISIRKEIAEVEKGNADVHN 983
            KRL+DYGFH PT+S+PVAGT+MIEPTESESKAELDRFCDALI+IR EI E+E+G AD  N
Sbjct: 835  KRLIDYGFHSPTVSFPVAGTMMIEPTESESKAELDRFCDALIAIRGEIREIEEGKADAEN 894

Query: 984  NVLKGAPHPPSLLMADAWTKPYSREYAAFPAAWLRGAKFWPTTGRVDNVYGDRNLVCTLL 1043
            NVLK APH   ++M+DAW  PYSRE A +P  +++ +KFWPT  R+D+ YGDRNLVC+ +
Sbjct: 895  NVLKNAPHTAGMVMSDAWDMPYSREKAVYPLEYVKNSKFWPTVRRIDSAYGDRNLVCSCI 954

Query: 1044 PASQAVEEQA 1053
            P     EE A
Sbjct: 955  PTEDYAEEAA 964


Lambda     K      H
   0.317    0.133    0.393 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 2375
Number of extensions: 88
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 1057
Length of database: 966
Length adjustment: 45
Effective length of query: 1012
Effective length of database: 921
Effective search space:   932052
Effective search space used:   932052
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (26.6 bits)

Align candidate Echvi_0744 Echvi_0744 (glycine dehydrogenase (decarboxylating))
to HMM TIGR00461 (gcvP: glycine dehydrogenase (EC 1.4.4.2))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR00461.hmm
# target sequence database:        /tmp/gapView.15801.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00461  [M=939]
Accession:   TIGR00461
Description: gcvP: glycine dehydrogenase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                            Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
          0 1437.6   0.1          0 1437.5   0.1    1.0  1  lcl|FitnessBrowser__Cola:Echvi_0744  Echvi_0744 glycine dehydrogenase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_0744  Echvi_0744 glycine dehydrogenase (decarboxylating)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1437.5   0.1         0         0       1     939 []      14     953 ..      14     953 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1437.5 bits;  conditional E-value: 0
                            TIGR00461   1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyiGkGyy 74 
                                          rh Gp++ ++ +ml  +G++++++li+q +pk+i+l +pl+l+ +++e + l++++k+a+knk +ks+iG Gyy
  lcl|FitnessBrowser__Cola:Echvi_0744  14 RHNGPSANDVSEMLSKIGASSIDELIDQTIPKAIQLDQPLNLPEAKSEAAFLKDFRKMAAKNKIYKSFIGLGYY 87 
                                          8************************************************************************* PP

                            TIGR00461  75 atilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaaaeamalsfrv 148
                                          +ti+p vi+rn+lenpgwytaytpyq+ei+qGrleal+nfqt+v+dltG+e+anaslldegtaaaeam + f  
  lcl|FitnessBrowser__Cola:Echvi_0744  88 DTITPGVILRNVLENPGWYTAYTPYQAEIAQGRLEALVNFQTMVMDLTGMELANASLLDEGTAAAEAMNMLFAT 161
                                          ********************************************************************998876 PP

                            TIGR00461 149 ...skkkankfvvakdvhpqtlevvktraeplgievivddaskvk.kavdvlGvllqypatdGeildykalide 218
                                              kkka kf+v+++v  qt+e++ktra p+g+ ++++  ++++ +  +++Gvllqyp ++Ge  dykal+++
  lcl|FitnessBrowser__Cola:Echvi_0744 162 rprDKKKATKFFVDEKVFIQTKEILKTRALPIGVTLVEGSLNELNlEDPELYGVLLQYPNAEGEAIDYKALVEK 235
                                          3336889***********************************9972567999********************** PP

                            TIGR00461 219 lksrkalvsvaadllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkdeykrklpGrivGvskdal 292
                                          +k++++  + +adllaltlltppg++Gad+v+G++qrfGvp+G+GGphaa+fa+kd ykr++pGri+G+s d+ 
  lcl|FitnessBrowser__Cola:Echvi_0744 236 AKQHNVTTAFSADLLALTLLTPPGEMGADVVVGTTQRFGVPMGFGGPHAAYFATKDAYKRQVPGRIIGISVDKD 309
                                          ************************************************************************** PP

                            TIGR00461 293 GntalrlalqtreqhirrdkatsnictaqvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyelr 366
                                          Gn a r+alqtreqhi+r++atsnictaqvlla++a +yavyhGpkGlk+ia +i+ l+++ a+gl + ++e +
  lcl|FitnessBrowser__Cola:Echvi_0744 310 GNKAYRMALQTREQHIKRERATSNICTAQVLLAVMAGMYAVYHGPKGLKDIALKIHGLAKLTAQGLAKLGFEQE 383
                                          ************************************************************************** PP

                            TIGR00461 367 nktyfdtltvevgekaasevlkaaeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelse 440
                                          n++yfdtl+++v +   s+++  a ++e+n+r   ++ v +a+de+ t edv+++++v+a     + ++  l +
  lcl|FitnessBrowser__Cola:Echvi_0744 384 NEHYFDTLKIKVDDVKQSKIKAFALSHEMNFR-YEPGYVYLAFDEAKTMEDVQEIIEVFARTTHSSADVVDLAS 456
                                          ******************************88.5799************************9999999999999 PP

                            TIGR00461 441 dvan...sfpaellrddeilrdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwp 511
                                           v +    +   l+r+++++ + +fn +hse e+lry++rle++dl+l +smi lGsctmklnataem+p+twp
  lcl|FitnessBrowser__Cola:Echvi_0744 457 MVDHlsfEVSDGLRRTSDYMDHMIFNAFHSEHEMLRYIKRLENRDLSLVHSMISLGSCTMKLNATAEMIPVTWP 530
                                          998883345678************************************************************** PP

                            TIGR00461 512 efaeihpfapaeqveGykeliaqlekwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclipa 585
                                          ef+++hpf p +q+ Gy  l+ +l +wl+eitGf   slqpnsGaqGe+aGl vir yhesrge hrni lip 
  lcl|FitnessBrowser__Cola:Echvi_0744 531 EFGQLHPFVPQDQAAGYYALFQDLRNWLSEITGFAETSLQPNSGAQGEFAGLMVIRAYHESRGESHRNIALIPS 604
                                          ************************************************************************** PP

                            TIGR00461 586 sahGtnpasaamaGlkvvpvkcdkeGnidlvdlkakaekagdelaavmvtypstyGvfeetirevidivhrfGG 659
                                          sahGtnpasa+maG+kvv vkcd++Gnidl dlk+kaek+ ++l++ +vtypst+Gvfee+ire+++ivh+ GG
  lcl|FitnessBrowser__Cola:Echvi_0744 605 SAHGTNPASAVMAGMKVVIVKCDDKGNIDLADLKEKAEKHKENLSSFLVTYPSTHGVFEEAIREMCQIVHENGG 678
                                          ************************************************************************** PP

                            TIGR00461 660 qvyldGanmnaqvGltspgdlGadvchlnlhktfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesk 733
                                          qvy+dGanmnaqvGltspg +Gadvchlnlhktf+iphGGGGpgmgpi+v  hl  flp +     +  +g+++
  lcl|FitnessBrowser__Cola:Echvi_0744 679 QVYMDGANMNAQVGLTSPGVIGADVCHLNLHKTFCIPHGGGGPGMGPICVAKHLEEFLPSS----PLVKTGGQQ 748
                                          ************************************************************4....444579999 PP

                            TIGR00461 734 sigavsaapyGsasilpisymyikmmGaeGlkkasevailnanylakrlkdaykilfvgrdervahecildlre 807
                                           i a+saap+Gsasilpisy+yi+mmG eGlk+a++ ailnany+ +rl ++++ l++g ++r ahe+i+d+re
  lcl|FitnessBrowser__Cola:Echvi_0744 749 PISAISAAPFGSASILPISYAYIAMMGREGLKHATQTAILNANYIKARLGEFFPTLYTGAQGRAAHEMIVDFRE 822
                                          ************************************************************************** PP

                            TIGR00461 808 lkekagiealdvakrlldyGfhaptlsfpvaGtlmveptesesleeldrfidamiaikeeidavkaGeikledn 881
                                          +k+  g+e++d+akrl+dyGfh+pt+sfpvaGt+m+epteses+ eldrf+da+iai+ ei ++ +G+ ++e+n
  lcl|FitnessBrowser__Cola:Echvi_0744 823 FKAV-GVEVEDIAKRLIDYGFHSPTVSFPVAGTMMIEPTESESKAELDRFCDALIAIRGEIREIEEGKADAENN 895
                                          **98.********************************************************************* PP

                            TIGR00461 882 ilknaphslqslivaewadpysreeaaypapvlkyfkfwptvarlddtyGdrnlvcsc 939
                                          +lknaph++  ++   w  pysre+a+yp+ ++k+ kfwptv+r+d +yGdrnlvcsc
  lcl|FitnessBrowser__Cola:Echvi_0744 896 VLKNAPHTAGMVMSDAWDMPYSREKAVYPLEYVKNSKFWPTVRRIDSAYGDRNLVCSC 953
                                          ********99999999999*************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (939 nodes)
Target sequences:                          1  (966 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.06u 0.02s 00:00:00.08 Elapsed: 00:00:00.08
# Mc/sec: 11.04
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources