Alignments for a candidate for gcvP in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvP in Pseudomonas putida KT2440

Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate PP_0988 PP_0988 glycine dehydrogenase

Query= reanno::pseudo6_N2E2:Pf6N2E2_5558
         (953 letters)



>FitnessBrowser__Putida:PP_0988
          Length = 951

 Score = 1681 bits (4352), Expect = 0.0
 Identities = 838/952 (88%), Positives = 887/952 (93%), Gaps = 4/952 (0%)

Query: 1   MTVNLGTANEFIARHIGPRASDEQAMLERLGYDSLEALSASVIPESIKGTSVLDMGDGQS 60
           MT+NLGTANEFIARHIGPRA+DEQAML  LG+DSL+A++A+VIP+SIKGTSVL   DGQS
Sbjct: 1   MTINLGTANEFIARHIGPRAADEQAMLTALGFDSLDAMTAAVIPDSIKGTSVLGSHDGQS 60

Query: 61  EADALASIKAIAAKNQLFKTYIGQGYYNCHTPAPILRNLLENPAWYTAYTPYQPEISQGR 120
           EADALA++KAIA KNQLFK+YIGQGYYN HTPAPILRNLLENPAWYTAYTPYQPEISQGR
Sbjct: 61  EADALAALKAIAGKNQLFKSYIGQGYYNTHTPAPILRNLLENPAWYTAYTPYQPEISQGR 120

Query: 121 LEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSNAFFASVHSHPQT 180
           LEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNK S+AFFASVH HPQT
Sbjct: 121 LEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKSSHAFFASVHCHPQT 180

Query: 181 LDVLRTRAEPLGIDVVVGDERELSDVSGFFGALLQYPASNGDLFDYRELTERFHTANALV 240
           LDVLRTRAEPLGI+VVVGDEREL DVS FFGALLQYPASNG++FDYRE+ +RFH ANALV
Sbjct: 181 LDVLRTRAEPLGIEVVVGDERELGDVSAFFGALLQYPASNGEVFDYREVVQRFHAANALV 240

Query: 241 AVAADLLALTLLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVG 300
           AVAADLLALTLLTPPGEF ADVAIGSAQRFGVPLGFGGPHAAYF+T+DAFKRDMPGRLVG
Sbjct: 241 AVAADLLALTLLTPPGEFDADVAIGSAQRFGVPLGFGGPHAAYFATRDAFKRDMPGRLVG 300

Query: 301 VSVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLVQIANR 360
           VS+DRFGK ALRLAMQTREQHIRREKATSNICTAQVLLANIASM+AVYHGP GL +IA R
Sbjct: 301 VSIDRFGKTALRLAMQTREQHIRREKATSNICTAQVLLANIASMFAVYHGPAGLKRIAER 360

Query: 361 IHHLTAILAKGLGALGLSVEQESFFDTLTLRTGAQTAALHDKARAQRINLRVVDAERLGL 420
            H LTAILA GL ALG+ V   S FDTLTL TG  TA+LHDKARAQ INLR +DA  +GL
Sbjct: 361 THALTAILAAGLKALGVQVVGASAFDTLTLATGTATASLHDKARAQGINLRQIDAAHVGL 420

Query: 421 SLDETTSQADVEALLRLIGNLMADGKAVPDFAALAASVQSHIPAELVRQSAILSHPVFNR 480
           SLDET++QADVE+L +L+G   A     PDF ALAAS  S +PA L+RQSAIL HPVFNR
Sbjct: 421 SLDETSTQADVESLWQLLGGEQAQ----PDFTALAASTGSLLPAALLRQSAILEHPVFNR 476

Query: 481 YHSETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQ 540
           YHSETELMRYLR+LADKDLALDR+MIPLGSCTMKLNAASEMIPVTWAEFG LHPFAPAEQ
Sbjct: 477 YHSETELMRYLRRLADKDLALDRSMIPLGSCTMKLNAASEMIPVTWAEFGNLHPFAPAEQ 536

Query: 541 SAGYQQLTDELEAMLCAATGYDAVSLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIP 600
           S GY Q+T ELEAMLCAATGYDAVSLQPNAGSQGEYAGLLAIRAYH+SRGE  RDICLIP
Sbjct: 537 SQGYLQMTTELEAMLCAATGYDAVSLQPNAGSQGEYAGLLAIRAYHRSRGEGHRDICLIP 596

Query: 601 SSAHGTNPATAHMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFE 660
           SSAHGTNPATAHMAGMRVVVTACDARGNVD+EDLRAKAIEHRE LAA+MITYPSTHGVFE
Sbjct: 597 SSAHGTNPATAHMAGMRVVVTACDARGNVDVEDLRAKAIEHRERLAAIMITYPSTHGVFE 656

Query: 661 EGIREICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGV 720
           E I EIC IIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGV
Sbjct: 657 EAIGEICAIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGV 716

Query: 721 GPIGVKSHLAPFLPGHASMERKQGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAI 780
           GPIGVKSHLAPFLPGHA +E  QGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQ+AI
Sbjct: 717 GPIGVKSHLAPFLPGHAQLENTQGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQMAI 776

Query: 781 LNANYIARRLEEHYPVLYSGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPT 840
           LNANYIARRLEEHYPVLY+G NGLVAHECILDLRPLKD+SGISVDDVAKRLIDFGFHAPT
Sbjct: 777 LNANYIARRLEEHYPVLYTGGNGLVAHECILDLRPLKDTSGISVDDVAKRLIDFGFHAPT 836

Query: 841 MSFPVAGTLMIEPTESESKEELDRFCDAMICIREEIRAVENGSLDKDDNPLKNAPHTAAE 900
           MSFPVAGTLMIEPTESESKEELDRFC+AMI IREEIRAVE+GSLDKDDNPLKNAPHTAAE
Sbjct: 837 MSFPVAGTLMIEPTESESKEELDRFCNAMIQIREEIRAVEDGSLDKDDNPLKNAPHTAAE 896

Query: 901 IVGEWTHPYSREQAVYPVASLIDGKYWPPVGRVDNVFGDRNLVCACPSIESY 952
           +VGEWTH YSREQAVYP+ASL++GKYWPPVGRVDNVFGDRNLVCACPSIESY
Sbjct: 897 LVGEWTHGYSREQAVYPLASLVEGKYWPPVGRVDNVFGDRNLVCACPSIESY 948


Lambda     K      H
   0.319    0.135    0.398 

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: 2500
Number of extensions: 88
Number of successful extensions: 3
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: 953
Length of database: 951
Length adjustment: 44
Effective length of query: 909
Effective length of database: 907
Effective search space:   824463
Effective search space used:   824463
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 PP_0988 PP_0988 (glycine dehydrogenase)
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.6578.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 1500.0   0.0          0 1499.8   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_0988  PP_0988 glycine dehydrogenase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_0988  PP_0988 glycine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1499.8   0.0         0         0       1     939 []      14     942 ..      14     942 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1499.8 bits;  conditional E-value: 0
                           TIGR00461   1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyiGkGyya 75 
                                         rh+Gp +a+ + ml +lGfd+l+a++  ++p++i+ +  l  +  ++e +ala lk+ia kn+ +ksyiG+Gyy+
  lcl|FitnessBrowser__Putida:PP_0988  14 RHIGPRAADEQAMLTALGFDSLDAMTAAVIPDSIKGTSVLGSHDGQSEADALAALKAIAGKNQLFKSYIGQGYYN 88 
                                         9************************************************************************** PP

                           TIGR00461  76 tilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaaaeamalsfrvsk 150
                                         t +p  i+rnllenp wytaytpyqpeisqGrleallnfqt+++dltGl++anasllde+taaaeam +++r+sk
  lcl|FitnessBrowser__Putida:PP_0988  89 THTPAPILRNLLENPAWYTAYTPYQPEISQGRLEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSK 163
                                         *************************************************************************** PP

                           TIGR00461 151 kk.ankfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdGeildykalidelksrka 224
                                         +k + +f+ + ++hpqtl+v++traeplgiev+v+d +++ +    +G+llqypa++Ge++dy++++++ +  +a
  lcl|FitnessBrowser__Putida:PP_0988 164 NKsSHAFFASVHCHPQTLDVLRTRAEPLGIEVVVGDERELGDVSAFFGALLQYPASNGEVFDYREVVQRFHAANA 238
                                         **7889999****************************************************************** PP

                           TIGR00461 225 lvsvaadllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkdeykrklpGrivGvskdalGntalrl 299
                                         lv+vaadllaltlltppg++ ad+++GsaqrfGvplG+GGphaa+fa++d +kr +pGr+vGvs d+ G+talrl
  lcl|FitnessBrowser__Putida:PP_0988 239 LVAVAADLLALTLLTPPGEFDADVAIGSAQRFGVPLGFGGPHAAYFATRDAFKRDMPGRLVGVSIDRFGKTALRL 313
                                         *************************************************************************** PP

                           TIGR00461 300 alqtreqhirrdkatsnictaqvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtl 374
                                         a+qtreqhirr+katsnictaqvllan+as++avyhGp Glk+ia+r + lt+ilaaglk  + ++  +  fdtl
  lcl|FitnessBrowser__Putida:PP_0988 314 AMQTREQHIRREKATSNICTAQVLLANIASMFAVYHGPAGLKRIAERTHALTAILAAGLKALGVQVVGASAFDTL 388
                                         *************************************************************************** PP

                           TIGR00461 375 tvevgekaasevlkaaeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelsedvansfpae 449
                                         t+  g  +a ++  +a++++inlr +++++vg++ldet t++dv+ l+++l g++    +   l     + +pa+
  lcl|FitnessBrowser__Putida:PP_0988 389 TLATGTATA-SLHDKARAQGINLRQIDAAHVGLSLDETSTQADVESLWQLLGGEQ-AQPDFTALAASTGSLLPAA 461
                                         **9998887.789999*************************************87.555888999999999**** PP

                           TIGR00461 450 llrddeilrdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeq 524
                                         llr++ il+++vfnryhsetel+ryl rl  kdlal++smiplGsctmklna+ em+p+tw ef+++hpfapaeq
  lcl|FitnessBrowser__Putida:PP_0988 462 LLRQSAILEHPVFNRYHSETELMRYLRRLADKDLALDRSMIPLGSCTMKLNAASEMIPVTWAEFGNLHPFAPAEQ 536
                                         *************************************************************************** PP

                           TIGR00461 525 veGykeliaqlekwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaG 599
                                         ++Gy ++ ++le+ l+  tG+da+slqpn+G+qGeyaGl +ir yh srge+hr+iclip sahGtnpa+a+maG
  lcl|FitnessBrowser__Putida:PP_0988 537 SQGYLQMTTELEAMLCAATGYDAVSLQPNAGSQGEYAGLLAIRAYHRSRGEGHRDICLIPSSAHGTNPATAHMAG 611
                                         *************************************************************************** PP

                           TIGR00461 600 lkvvpvkcdkeGnidlvdlkakaekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGl 674
                                         ++vv+ +cd  Gn+d++dl+aka ++ ++laa+m+typst+Gvfee+i+e++ i+h  GGqvy+dGanmna vGl
  lcl|FitnessBrowser__Putida:PP_0988 612 MRVVVTACDARGNVDVEDLRAKAIEHRERLAAIMITYPSTHGVFEEAIGEICAIIHDNGGQVYIDGANMNAMVGL 686
                                         *************************************************************************** PP

                           TIGR00461 675 tspgdlGadvchlnlhktfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasil 749
                                         ++pg++G dv+hlnlhktf+iphGGGGpg+gpigvkshlapflp++      +    ++++gav aap+Gsasil
  lcl|FitnessBrowser__Putida:PP_0988 687 CAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGVKSHLAPFLPGHA-----Q---LENTQGAVCAAPFGSASIL 753
                                         *********************************************42.....3...35679************** PP

                           TIGR00461 750 pisymyikmmGaeGlkkasevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrll 824
                                         pi++myi+mmG  Glk+as++ailnany+a+rl+++y++l++g ++ vahecildlr+lk+ +gi++ dvakrl+
  lcl|FitnessBrowser__Putida:PP_0988 754 PITWMYIRMMGGAGLKRASQMAILNANYIARRLEEHYPVLYTGGNGLVAHECILDLRPLKDTSGISVDDVAKRLI 828
                                         *************************************************************************** PP

                           TIGR00461 825 dyGfhaptlsfpvaGtlmveptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivaewa 899
                                         d+Gfhapt+sfpvaGtlm+epteses+eeldrf++ami i+eei av  G ++++dn+lknaph+   ++v+ew+
  lcl|FitnessBrowser__Putida:PP_0988 829 DFGFHAPTMSFPVAGTLMIEPTESESKEELDRFCNAMIQIREEIRAVEDGSLDKDDNPLKNAPHT-AAELVGEWT 902
                                         ****************************************************************6.56789**** PP

                           TIGR00461 900 dpysreeaaypapvlkyfkfwptvarlddtyGdrnlvcsc 939
                                         + ysre+a+yp++ l + k+wp v+r+d+++Gdrnlvc+c
  lcl|FitnessBrowser__Putida:PP_0988 903 HGYSREQAVYPLASLVEGKYWPPVGRVDNVFGDRNLVCAC 942
                                         ***************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (939 nodes)
Target sequences:                          1  (951 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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 12.96
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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