GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gcvP in Pseudomonas fluorescens FW300-N1B4

Align glycine dehydrogenase [decarboxylating]; EC 1.4.4.2 (characterized)
to candidate Pf1N1B4_2236 Glycine dehydrogenase [decarboxylating] (glycine cleavage system P protein) (EC 1.4.4.2)

Query= CharProtDB::CH_003480
         (957 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 Glycine dehydrogenase
           [decarboxylating] (glycine cleavage system P protein)
           (EC 1.4.4.2)
          Length = 957

 Score = 1261 bits (3264), Expect = 0.0
 Identities = 631/957 (65%), Positives = 754/957 (78%), Gaps = 8/957 (0%)

Query: 4   TLSQLENSGAFIERHIGPDAAQQQEMLNAVGAQSLNALTGQIVPKDIQLATPPQVGAPAT 63
           +LSQL +   F+ RH+GPDAA+QQ ML+++G  S   L  Q VP  I+L  P  +     
Sbjct: 6   SLSQLRDPNTFLRRHLGPDAAEQQAMLDSLGLGSRVELIEQTVPPGIRLNRPLDLPPALD 65

Query: 64  EYAALAELKAIASRNKRFTSYIGMGYTAVQLPPVILRNMLENPGWYTAYTPYQPEVSQGR 123
           E AALA+L+  A +N+ +TS IGMGY     P VILRN+LENPGWYTAYTPYQPE++QGR
Sbjct: 66  EEAALAKLRGYAEQNQIWTSLIGMGYHGTLTPAVILRNVLENPGWYTAYTPYQPEIAQGR 125

Query: 124 LEALLNFQQVTLDLTGLDMASASLLDEATAAAEAMAMAKRVSKLKNANRFFVASDVHPQT 183
           LEALLNFQQ+T+DLTGL++A+ASLLDEATAAAEAMA+AKRV+K ++ N FFV  + HPQT
Sbjct: 126 LEALLNFQQLTIDLTGLELANASLLDEATAAAEAMALAKRVAKSRS-NLFFVDENCHPQT 184

Query: 184 LDVVRTRAETFGFEVIVDDAQKVLDHQDVFGVLLQQVGTTGEIHDYTALISELKSRKIVV 243
           + VVRTRAE FGFE+I+D    +  HQ VFG LLQ   T GE+ D   LI  L +++ +V
Sbjct: 185 ISVVRTRAEGFGFELIIDAVDNLKQHQ-VFGALLQYPDTHGEVRDLRPLIDHLHAQQALV 243

Query: 244 SVAADIMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEYKRSMPGRIIG 303
            VA D+++L+LLT PG+ GAD+VFGS+QRFGVPMGYGGPHAAFFA++DEYKR++PGRIIG
Sbjct: 244 CVATDLLSLLLLTPPGELGADVVFGSSQRFGVPMGYGGPHAAFFASRDEYKRAIPGRIIG 303

Query: 304 VSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVYHGPVGLKRIANR 363
           VSKDA GN ALRMA+QTREQHIRREKANSNICT+QVLLANIAS YAVYHGP GLKRIA R
Sbjct: 304 VSKDARGNVALRMALQTREQHIRREKANSNICTAQVLLANIASFYAVYHGPEGLKRIAQR 363

Query: 364 IHRLTDILAAGLQQKGLKLRHAHYFDTLCVEVAD-KAGVLTRAEAAEINLRSDILNAVGI 422
           +HRLT ILAAGL++ G+   + ++FDTL +EV   +  ++  A+AA+INLR      +G+
Sbjct: 364 VHRLTCILAAGLERHGITRLNQNFFDTLTLEVGGTQTAIIESAQAAQINLRILGRGQLGL 423

Query: 423 TLDETTTRENVMQLFNVLLGDNHGLDIDTLDKDVAHDSRSIQPAMLRDDEILTHPVFNRY 482
           +LDET     V +LF+V LG +HGL++D LD +       I   + R    L HPVFN +
Sbjct: 424 SLDETCDETTVAKLFDVFLGADHGLNVDDLDAETLVSG--IPAGLQRSTSYLRHPVFNAH 481

Query: 483 HSETEMMRYMHSLERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPPEQA 542
           HSETEM+RY+  LE KDLALNQ+MIPLGSCTMKLNA +EMIPITWP+FA LHPF P EQ 
Sbjct: 482 HSETEMLRYLKQLENKDLALNQSMIPLGSCTMKLNATSEMIPITWPQFANLHPFVPKEQV 541

Query: 543 EGYQQMIAQLADWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICLIPA 602
            GY  MIA+L  WL  +TG+DA+CMQPNSGAQGEYAGLLAIR YHESR++G RDICLIP+
Sbjct: 542 VGYSLMIAELERWLCAITGFDAICMQPNSGAQGEYAGLLAIRKYHESRHQGARDICLIPS 601

Query: 603 SAHGTNPASAHMAGMQVVVVACDKNGNIDLTDLRAKAEQAGDNLSCIMVTYPSTHGVYEE 662
           SAHGTNPASA MAGM+VV+V CD+ GN+DL DL+ KA +AGD L+C+M TYPSTHGVYEE
Sbjct: 602 SAHGTNPASAQMAGMRVVIVECDEGGNVDLDDLKEKATEAGDKLACLMATYPSTHGVYEE 661

Query: 663 TIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPGMG 722
            I E+CEV+H  GGQVY+DGAN+NAQVG+  P  IGADVSH+NLHKTFCIPHGGGGPGMG
Sbjct: 662 GISEICEVIHSHGGQVYMDGANLNAQVGLARPADIGADVSHMNLHKTFCIPHGGGGPGMG 721

Query: 723 PIGVKAHLAPFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKKAS 782
           PIGV+AHLAPFV  H VV I+G L   GAVSAAP+GSASILPISWMYI MMG + L  AS
Sbjct: 722 PIGVRAHLAPFVANHPVVPIDGPLPENGAVSAAPWGSASILPISWMYIAMMGPQ-LADAS 780

Query: 783 QVAILNANYIASRLQDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLIDYGF 842
           +VAIL ANY+A  L  AFPVLYTGR+ RVAHECILD+RPLK +TGISE D+AKRL+DYGF
Sbjct: 781 EVAILAANYLAQHLAGAFPVLYTGRNERVAHECILDLRPLKAQTGISEEDVAKRLMDYGF 840

Query: 843 HAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRAEIDQVKAGVWPLEDNPLVNAPH 902
           HAPTMSFPV GTLMVEPTESESK ELDRFI AML+IRAEI +V+ G WP EDNPL  +PH
Sbjct: 841 HAPTMSFPVPGTLMVEPTESESKAELDRFIGAMLSIRAEITEVQNGNWPAEDNPLKRSPH 900

Query: 903 IQSELVAEWAHPYSREVAVFPAG--VADKYWPTVKRLDDVYGDRNLFCSCVPISEYQ 957
             +++   W  PYS E AV P     A KYWP V R+D+VYGDRNLFC+CVP+ EY+
Sbjct: 901 TLADITGVWERPYSIERAVTPDAHTKAHKYWPVVNRVDNVYGDRNLFCACVPVDEYR 957


Lambda     K      H
   0.319    0.134    0.395 

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: 2345
Number of extensions: 84
Number of successful extensions: 7
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: 957
Length of database: 957
Length adjustment: 44
Effective length of query: 913
Effective length of database: 913
Effective search space:   833569
Effective search space used:   833569
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (26.6 bits)

Align candidate Pf1N1B4_2236 (Glycine dehydrogenase [decarboxylating] (glycine cleavage system P protein) (EC 1.4.4.2))
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.1129.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 1539.8   0.0          0 1539.6   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236  Glycine dehydrogenase [decarboxy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236  Glycine dehydrogenase [decarboxylating] (glycine cleavage system P pro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1539.6   0.0         0         0       1     939 []      19     950 ..      19     950 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1539.6 bits;  conditional E-value: 0
                                      TIGR00461   1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkk 64 
                                                    rhlGpd+aeq+ ml++lG  +  +lieq vp+ irl+rpl l+ +  e +ala+l+  a++n+ 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236  19 RHLGPDAAEQQAMLDSLGLGSRVELIEQTVPPGIRLNRPLDLPPALDEEAALAKLRGYAEQNQI 82 
                                                    9*************************************************************** PP

                                      TIGR00461  65 vksyiGkGyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevan 128
                                                     +s iG+Gy +t++p vi+rn+lenpgwytaytpyqpei+qGrleallnfq++++dltGle+an
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236  83 WTSLIGMGYHGTLTPAVILRNVLENPGWYTAYTPYQPEIAQGRLEALLNFQQLTIDLTGLELAN 146
                                                    **************************************************************** PP

                                      TIGR00461 129 aslldegtaaaeamalsfrvskkkankfvvakdvhpqtlevvktraeplgievivddaskvkka 192
                                                    asllde+taaaeamal++rv+k+++n f+v++++hpqt++vv+trae +g+e+i+d ++++k++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 147 ASLLDEATAAAEAMALAKRVAKSRSNLFFVDENCHPQTISVVRTRAEGFGFELIIDAVDNLKQH 210
                                                    ******************************************************9888888776 PP

                                      TIGR00461 193 vdvlGvllqypatdGeildykalidelksrkalvsvaadllaltlltppgklGadivlGsaqrf 256
                                                     +v+G+llqyp t+Ge+ d++ lid+l+ ++alv+va+dll+l lltppg+lGad+v+Gs+qrf
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 211 -QVFGALLQYPDTHGEVRDLRPLIDHLHAQQALVCVATDLLSLLLLTPPGELGADVVFGSSQRF 273
                                                    .6************************************************************** PP

                                      TIGR00461 257 GvplGyGGphaaffavkdeykrklpGrivGvskdalGntalrlalqtreqhirrdkatsnicta 320
                                                    Gvp+GyGGphaaffa++deykr +pGri+Gvskda Gn alr+alqtreqhirr+ka+snicta
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 274 GVPMGYGGPHAAFFASRDEYKRAIPGRIIGVSKDARGNVALRMALQTREQHIRREKANSNICTA 337
                                                    **************************************************************** PP

                                      TIGR00461 321 qvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaas 384
                                                    qvllan+as yavyhGp Glk+ia+r++rlt ilaagl+r++    n+++fdtlt+evg   + 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 338 QVLLANIASFYAVYHGPEGLKRIAQRVHRLTCILAAGLERHGITRLNQNFFDTLTLEVGGTQT- 400
                                                    ***********************************************************8877. PP

                                      TIGR00461 385 evlkaaeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelsedvan.sfp 447
                                                    ++ ++a++a+inlr +  +++g++ldet  +  v +l++v++g d +gl+++ l+ +     +p
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 401 AIIESAQAAQINLRILGRGQLGLSLDETCDETTVAKLFDVFLGAD-HGLNVDDLDAETLVsGIP 463
                                                    89999**************************************87.********99876537** PP

                                      TIGR00461 448 aellrddeilrdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwp 511
                                                    a l+r+  +lr++vfn +hsete+lryl++le+kdlalnqsmiplGsctmklnat em+pitwp
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 464 AGLQRSTSYLRHPVFNAHHSETEMLRYLKQLENKDLALNQSMIPLGSCTMKLNATSEMIPITWP 527
                                                    **************************************************************** PP

                                      TIGR00461 512 efaeihpfapaeqveGykeliaqlekwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrge 575
                                                    +fa++hpf p eqv Gy  +ia+le wl+ itGfdai++qpnsGaqGeyaGl +ir+yhesr +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 528 QFANLHPFVPKEQVVGYSLMIAELERWLCAITGFDAICMQPNSGAQGEYAGLLAIRKYHESRHQ 591
                                                    **************************************************************** PP

                                      TIGR00461 576 ehrniclipasahGtnpasaamaGlkvvpvkcdkeGnidlvdlkakaekagdelaavmvtypst 639
                                                    + r+iclip sahGtnpasa+maG++vv v+cd+ Gn+dl dlk+ka +agd+la++m typst
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 592 GARDICLIPSSAHGTNPASAQMAGMRVVIVECDEGGNVDLDDLKEKATEAGDKLACLMATYPST 655
                                                    **************************************************************** PP

                                      TIGR00461 640 yGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvchlnlhktfsiphGGGGpg 703
                                                    +Gv+ee+i e+++++h+ GGqvy+dGan+naqvGl++p+d+Gadv+h+nlhktf+iphGGGGpg
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 656 HGVYEEGISEICEVIHSHGGQVYMDGANLNAQVGLARPADIGADVSHMNLHKTFCIPHGGGGPG 719
                                                    **************************************************************** PP

                                      TIGR00461 704 mgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymyikmmGaeGlkka 767
                                                    mgpigv++hlapf+ +   + vv ++g   + gavsaap+Gsasilpis+myi+mmG++ l  a
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 720 MGPIGVRAHLAPFVAN---HPVVPIDGPLPENGAVSAAPWGSASILPISWMYIAMMGPQ-LADA 779
                                                    ****************...78999**********************************8.99** PP

                                      TIGR00461 768 sevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGfhap 831
                                                    sevail+anyla+ l  a+++l++gr+ervahecildlr+lk+++gi+++dvakrl+dyGfhap
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 780 SEVAILAANYLAQHLAGAFPVLYTGRNERVAHECILDLRPLKAQTGISEEDVAKRLMDYGFHAP 843
                                                    **************************************************************** PP

                                      TIGR00461 832 tlsfpvaGtlmveptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqsliv 895
                                                    t+sfpv+Gtlmvepteses+ eldrfi am++i++ei +v++G++++edn+lk +ph+l + i+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 844 TMSFPVPGTLMVEPTESESKAELDRFIGAMLSIRAEITEVQNGNWPAEDNPLKRSPHTLAD-IT 906
                                                    *********************************************************8875.9* PP

                                      TIGR00461 896 aewadpysreeaaypapvlkyfkfwptvarlddtyGdrnlvcsc 939
                                                    + w  pys e a+ p + +k +k+wp v+r+d++yGdrnl+c+c
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 907 GVWERPYSIERAVTPDAHTKAHKYWPVVNRVDNVYGDRNLFCAC 950
                                                    *******************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (939 nodes)
Target sequences:                          1  (957 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: 0.08u 0.03s 00:00:00.11 Elapsed: 00:00:00.10
# Mc/sec: 8.29
//
[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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

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

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:

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. Gaps may be due to:

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, or view the source code.

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