Alignments for a candidate for putA in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Pseudomonas stutzeri RCH2

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate GFF3021 Psest_3079 delta-1-pyrroline-5-carboxylate dehydrogenase (PutA C-terminal domain)

Query= reanno::psRCH2:GFF3021
         (1053 letters)



>FitnessBrowser__psRCH2:GFF3021
          Length = 1053

 Score = 2078 bits (5384), Expect = 0.0
 Identities = 1053/1053 (100%), Positives = 1053/1053 (100%)

Query: 1    MFKAGHVLDGAFANQKAAEFFPAISANYSVDEAQYLTELLQLADPGEAGIAAIRERARSL 60
            MFKAGHVLDGAFANQKAAEFFPAISANYSVDEAQYLTELLQLADPGEAGIAAIRERARSL
Sbjct: 1    MFKAGHVLDGAFANQKAAEFFPAISANYSVDEAQYLTELLQLADPGEAGIAAIRERARSL 60

Query: 61   IEAVRGRDNAVDTLDALLRQYSLDTQEGLMLMCLAEALLRVPDAATADALIRDKLNAAEW 120
            IEAVRGRDNAVDTLDALLRQYSLDTQEGLMLMCLAEALLRVPDAATADALIRDKLNAAEW
Sbjct: 61   IEAVRGRDNAVDTLDALLRQYSLDTQEGLMLMCLAEALLRVPDAATADALIRDKLNAAEW 120

Query: 121  ERHLGQSDNVLVNFAAWGLVMTGKVVDPETADGRPKNVIGRLLKRSGEPVIRGAMNQAMK 180
            ERHLGQSDNVLVNFAAWGLVMTGKVVDPETADGRPKNVIGRLLKRSGEPVIRGAMNQAMK
Sbjct: 121  ERHLGQSDNVLVNFAAWGLVMTGKVVDPETADGRPKNVIGRLLKRSGEPVIRGAMNQAMK 180

Query: 181  LMGKQFVLGRTISEALKNGRPEREKGYTYSFDMLGEAALTAEDAAKYMADYRQAVETVGA 240
            LMGKQFVLGRTISEALKNGRPEREKGYTYSFDMLGEAALTAEDAAKYMADYRQAVETVGA
Sbjct: 181  LMGKQFVLGRTISEALKNGRPEREKGYTYSFDMLGEAALTAEDAAKYMADYRQAVETVGA 240

Query: 241  EPQVGKGPRPSVSIKLSALHPRYELAQRERVLTELFGSVRELAILARRLNVGITIDAEEA 300
            EPQVGKGPRPSVSIKLSALHPRYELAQRERVLTELFGSVRELAILARRLNVGITIDAEEA
Sbjct: 241  EPQVGKGPRPSVSIKLSALHPRYELAQRERVLTELFGSVRELAILARRLNVGITIDAEEA 300

Query: 301  DRLELSLELYEKLLRDPAIAGWGEFGLVIQAYSKRCLPVLVWLTLLGRELGERIPLRLVK 360
            DRLELSLELYEKLLRDPAIAGWGEFGLVIQAYSKRCLPVLVWLTLLGRELGERIPLRLVK
Sbjct: 301  DRLELSLELYEKLLRDPAIAGWGEFGLVIQAYSKRCLPVLVWLTLLGRELGERIPLRLVK 360

Query: 361  GAYWDSEIKQCQVQGLDGYPVYTRKEGTDTSYLACARYLLSEHTRGVIYPQFASHNAHTV 420
            GAYWDSEIKQCQVQGLDGYPVYTRKEGTDTSYLACARYLLSEHTRGVIYPQFASHNAHTV
Sbjct: 361  GAYWDSEIKQCQVQGLDGYPVYTRKEGTDTSYLACARYLLSEHTRGVIYPQFASHNAHTV 420

Query: 421  SCILAMAEETAQPREFEFQRLHGMGDALYDTVIEKYARNVRIYAPVGAHKDLLPYLVRRL 480
            SCILAMAEETAQPREFEFQRLHGMGDALYDTVIEKYARNVRIYAPVGAHKDLLPYLVRRL
Sbjct: 421  SCILAMAEETAQPREFEFQRLHGMGDALYDTVIEKYARNVRIYAPVGAHKDLLPYLVRRL 480

Query: 481  LENGANSSFVHQLVDPRVPVESLIDHPVTQLRRFAAPGNPRIPLPPALFGNRKNSQGINM 540
            LENGANSSFVHQLVDPRVPVESLIDHPVTQLRRFAAPGNPRIPLPPALFGNRKNSQGINM
Sbjct: 481  LENGANSSFVHQLVDPRVPVESLIDHPVTQLRRFAAPGNPRIPLPPALFGNRKNSQGINM 540

Query: 541  NIQNQWTELASAYQPFLERQWQAAPVISGRTLAGTPSEVRCPYELNKVVGQAQFASADQA 600
            NIQNQWTELASAYQPFLERQWQAAPVISGRTLAGTPSEVRCPYELNKVVGQAQFASADQA
Sbjct: 541  NIQNQWTELASAYQPFLERQWQAAPVISGRTLAGTPSEVRCPYELNKVVGQAQFASADQA 600

Query: 601  RQAIDRLAAYWPIWNATPVEARAAVLERLGDLLEQHRAELMALCTVEAGKSLQDGIDEVR 660
            RQAIDRLAAYWPIWNATPVEARAAVLERLGDLLEQHRAELMALCTVEAGKSLQDGIDEVR
Sbjct: 601  RQAIDRLAAYWPIWNATPVEARAAVLERLGDLLEQHRAELMALCTVEAGKSLQDGIDEVR 660

Query: 661  EAVDFCRYYAQQARLKLGREELKGPTGERNELFHEGRGVFVCVSPWNFPLAIYLGQITAA 720
            EAVDFCRYYAQQARLKLGREELKGPTGERNELFHEGRGVFVCVSPWNFPLAIYLGQITAA
Sbjct: 661  EAVDFCRYYAQQARLKLGREELKGPTGERNELFHEGRGVFVCVSPWNFPLAIYLGQITAA 720

Query: 721  LVAGNTVLAKPAEQTSLIAARALELMFEAGLPQEAIAFLPGDGATLGGVFCRDPRVVGVC 780
            LVAGNTVLAKPAEQTSLIAARALELMFEAGLPQEAIAFLPGDGATLGGVFCRDPRVVGVC
Sbjct: 721  LVAGNTVLAKPAEQTSLIAARALELMFEAGLPQEAIAFLPGDGATLGGVFCRDPRVVGVC 780

Query: 781  FTGSTDTARIINRQLAEKEGPIATLIAETGGQNAMIVDSTALPEQVIKDAVGSAFTSAGQ 840
            FTGSTDTARIINRQLAEKEGPIATLIAETGGQNAMIVDSTALPEQVIKDAVGSAFTSAGQ
Sbjct: 781  FTGSTDTARIINRQLAEKEGPIATLIAETGGQNAMIVDSTALPEQVIKDAVGSAFTSAGQ 840

Query: 841  RCSALRVLYVQRDIADRVIDLLKGAMAELRVGPTHLRENDIGPVIDQEAREGLLAHIQQL 900
            RCSALRVLYVQRDIADRVIDLLKGAMAELRVGPTHLRENDIGPVIDQEAREGLLAHIQQL
Sbjct: 841  RCSALRVLYVQRDIADRVIDLLKGAMAELRVGPTHLRENDIGPVIDQEAREGLLAHIQQL 900

Query: 901  KSEGRLIAEATVPAGLNGHFVAPVAFEIDGIHQLKKEHFGPVLHVVRYDAADLEKVVAAI 960
            KSEGRLIAEATVPAGLNGHFVAPVAFEIDGIHQLKKEHFGPVLHVVRYDAADLEKVVAAI
Sbjct: 901  KSEGRLIAEATVPAGLNGHFVAPVAFEIDGIHQLKKEHFGPVLHVVRYDAADLEKVVAAI 960

Query: 961  NGTGYGLTLGVHSRNEETAERIEQLARVGNLYVNRNQIGAVVGVQPFGGCRLSGTGPKAG 1020
            NGTGYGLTLGVHSRNEETAERIEQLARVGNLYVNRNQIGAVVGVQPFGGCRLSGTGPKAG
Sbjct: 961  NGTGYGLTLGVHSRNEETAERIEQLARVGNLYVNRNQIGAVVGVQPFGGCRLSGTGPKAG 1020

Query: 1021 GPSYLLRFANERTTSTNTTAVGGNASLLSLGDD 1053
            GPSYLLRFANERTTSTNTTAVGGNASLLSLGDD
Sbjct: 1021 GPSYLLRFANERTTSTNTTAVGGNASLLSLGDD 1053


Lambda     K      H
   0.319    0.136    0.396 

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: 3243
Number of extensions: 94
Number of successful extensions: 1
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: 1053
Length of database: 1053
Length adjustment: 45
Effective length of query: 1008
Effective length of database: 1008
Effective search space:  1016064
Effective search space used:  1016064
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: 58 (26.9 bits)

Align candidate GFF3021 Psest_3079 (delta-1-pyrroline-5-carboxylate dehydrogenase (PutA C-terminal domain))
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

# 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/TIGR01238.hmm
# target sequence database:        /tmp/gapView.27564.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01238  [M=500]
Accession:   TIGR01238
Description: D1pyr5carbox3: delta-1-pyrroline-5-carboxylate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.4e-211  688.0   0.2     5e-211  687.4   0.2    1.2  1  lcl|FitnessBrowser__psRCH2:GFF3021  Psest_3079 delta-1-pyrroline-5-c


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3021  Psest_3079 delta-1-pyrroline-5-carboxylate dehydrogenase (PutA C-terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  687.4   0.2    5e-211    5e-211       2     497 ..     528    1030 ..     527    1033 .. 0.98

  Alignments for each domain:
  == domain 1  score: 687.4 bits;  conditional E-value: 5e-211
                           TIGR01238    2 lygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvseadaa 74  
                                          l+g+ rkns+G++++++++  +l +  +  +++++qaap++++++ a g    v+ p++ +++vGq ++a+a+
  lcl|FitnessBrowser__psRCH2:GFF3021  528 LFGN-RKNSQGINMNIQNQWTELASAYQPFLERQWQAAPVISGRTLA-GTPSEVRCPYELNKVVGQAQFASAD 598 
                                          7898.************************************877766.66678******************** PP

                           TIGR01238   75 evqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryyak 147 
                                          ++++a+d   a  ++w+at+ + raa+lerl dlle+h  el+al+  eaGk+l++ i+evreavdf+ryya+
  lcl|FitnessBrowser__psRCH2:GFF3021  599 QARQAIDRLAAYWPIWNATPVEARAAVLERLGDLLEQHRAELMALCTVEAGKSLQDGIDEVREAVDFCRYYAQ 671 
                                          ************************************************************************* PP

                           TIGR01238  148 qvedvldeesaka............lGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaarave 208 
                                          q++ +l++e  k             +G++vc+spwnfplai++Gqi+aal+aGntv+akpaeqtsliaara+e
  lcl|FitnessBrowser__psRCH2:GFF3021  672 QARLKLGREELKGptgernelfhegRGVFVCVSPWNFPLAIYLGQITAALVAGNTVLAKPAEQTSLIAARALE 744 
                                          *********99989*********************************************************** PP

                           TIGR01238  209 llqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredapvpliaetGGqnamiv 281 
                                          l+ eaG+p  +i +lpG G+++G  +  d+r+ Gv ftGst++ar in++la++e + ++liaetGGqnamiv
  lcl|FitnessBrowser__psRCH2:GFF3021  745 LMFEAGLPQEAIAFLPGDGATLGGVFCRDPRVVGVCFTGSTDTARIINRQLAEKEGPIATLIAETGGQNAMIV 817 
                                          ************************************************************************* PP

                           TIGR01238  282 dstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeak 354 
                                          dstal+eqv++d + saf saGqrcsalrvl+vq+d+adrv++l+kGam el+vg  ++ + d+Gpvid+ea+
  lcl|FitnessBrowser__psRCH2:GFF3021  818 DSTALPEQVIKDAVGSAFTSAGQRCSALRVLYVQRDIADRVIDLLKGAMAELRVGPTHLRENDIGPVIDQEAR 890 
                                          ************************************************************************* PP

                           TIGR01238  355 qnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdki 427 
                                          + llahi+++k+ ++ +a+++  +     +g fvap++fe+d +++lkke fGpvlhvvry a +l+kvv  i
  lcl|FitnessBrowser__psRCH2:GFF3021  891 EGLLAHIQQLKSEGRLIAEATVPA---GLNGHFVAPVAFEIDGIHQLKKEHFGPVLHVVRYDAADLEKVVAAI 960 
                                          *********************998...678******************************************* PP

                           TIGR01238  428 nakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltr 497 
                                          n +GygltlGvhsr+eet  +ie+ a+vGn+yvnrn++GavvGvqpfGG  lsGtGpkaGGp yl r+ +
  lcl|FitnessBrowser__psRCH2:GFF3021  961 NGTGYGLTLGVHSRNEETAERIEQLARVGNLYVNRNQIGAVVGVQPFGGCRLSGTGPKAGGPSYLLRFAN 1030
                                          *******************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1053 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 19.22
//
[ok]

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

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Protein sequences (fasta format)
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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