Alignments for a candidate for putA in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Phaeobacter inhibens BS107

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate GFF1160 PGA1_c11750 bifunctional protein PutA

Query= reanno::Phaeo:GFF1160
         (1158 letters)



>FitnessBrowser__Phaeo:GFF1160
          Length = 1158

 Score = 2282 bits (5914), Expect = 0.0
 Identities = 1158/1158 (100%), Positives = 1158/1158 (100%)

Query: 1    MTAPQSKTTPEMPSAPTPEYSDALRYRIDAGTYVDQAQMRDQLFALANLDATDRSTISAN 60
            MTAPQSKTTPEMPSAPTPEYSDALRYRIDAGTYVDQAQMRDQLFALANLDATDRSTISAN
Sbjct: 1    MTAPQSKTTPEMPSAPTPEYSDALRYRIDAGTYVDQAQMRDQLFALANLDATDRSTISAN 60

Query: 61   AAALVRDIRGHSSPGLMEVFLAEYGLSTDEGVALMCLAEALLRVPDADTIDALIEDKIAP 120
            AAALVRDIRGHSSPGLMEVFLAEYGLSTDEGVALMCLAEALLRVPDADTIDALIEDKIAP
Sbjct: 61   AAALVRDIRGHSSPGLMEVFLAEYGLSTDEGVALMCLAEALLRVPDADTIDALIEDKIAP 120

Query: 121  SEWGKHLGKSTSSLVNASTWALMLTGKVLDEKRSPVSALRGAMKRLGEPVIRTAVSRAMK 180
            SEWGKHLGKSTSSLVNASTWALMLTGKVLDEKRSPVSALRGAMKRLGEPVIRTAVSRAMK
Sbjct: 121  SEWGKHLGKSTSSLVNASTWALMLTGKVLDEKRSPVSALRGAMKRLGEPVIRTAVSRAMK 180

Query: 181  EMGRQFVLGETIEGAMKRAAGMEAKGYTYSYDMLGEAARTEADAARYHLAYSRAISAIAA 240
            EMGRQFVLGETIEGAMKRAAGMEAKGYTYSYDMLGEAARTEADAARYHLAYSRAISAIAA
Sbjct: 181  EMGRQFVLGETIEGAMKRAAGMEAKGYTYSYDMLGEAARTEADAARYHLAYSRAISAIAA 240

Query: 241  ACNSADIRQNPGISVKLSALHPRYELAQETSVKEQLVPRLQALALLAKAAGMGLNVDAEE 300
            ACNSADIRQNPGISVKLSALHPRYELAQETSVKEQLVPRLQALALLAKAAGMGLNVDAEE
Sbjct: 241  ACNSADIRQNPGISVKLSALHPRYELAQETSVKEQLVPRLQALALLAKAAGMGLNVDAEE 300

Query: 301  ADRLSLSLEVIEEVISDPALAGWDGFGVVVQAYGPRTGAALDALYDMANRYDRRLMVRLV 360
            ADRLSLSLEVIEEVISDPALAGWDGFGVVVQAYGPRTGAALDALYDMANRYDRRLMVRLV
Sbjct: 301  ADRLSLSLEVIEEVISDPALAGWDGFGVVVQAYGPRTGAALDALYDMANRYDRRLMVRLV 360

Query: 361  KGAYWDTEVKRAQVEGVDGFPVFTHKSLTDVSYIANARKLLSITDRIYPQFATHNAHTVS 420
            KGAYWDTEVKRAQVEGVDGFPVFTHKSLTDVSYIANARKLLSITDRIYPQFATHNAHTVS
Sbjct: 361  KGAYWDTEVKRAQVEGVDGFPVFTHKSLTDVSYIANARKLLSITDRIYPQFATHNAHTVS 420

Query: 421  AILHMAKDTDKGAYEFQRLHGMGETLHNMVLEQNQTHCRIYAPVGAHRDLLAYLVRRLLE 480
            AILHMAKDTDKGAYEFQRLHGMGETLHNMVLEQNQTHCRIYAPVGAHRDLLAYLVRRLLE
Sbjct: 421  AILHMAKDTDKGAYEFQRLHGMGETLHNMVLEQNQTHCRIYAPVGAHRDLLAYLVRRLLE 480

Query: 481  NGANSSFVNQIVDENVPPELVAADPFAQVEDLTANLRKGPDLFQPERPNSIGFDLGHAPT 540
            NGANSSFVNQIVDENVPPELVAADPFAQVEDLTANLRKGPDLFQPERPNSIGFDLGHAPT
Sbjct: 481  NGANSSFVNQIVDENVPPELVAADPFAQVEDLTANLRKGPDLFQPERPNSIGFDLGHAPT 540

Query: 541  LAAIDAARAPWKSHSWAAEPLLAKAPETATTTDEPVRNPADLTTVGRVQTAGQAEIETAL 600
            LAAIDAARAPWKSHSWAAEPLLAKAPETATTTDEPVRNPADLTTVGRVQTAGQAEIETAL
Sbjct: 541  LAAIDAARAPWKSHSWAAEPLLAKAPETATTTDEPVRNPADLTTVGRVQTAGQAEIETAL 600

Query: 601  SAATPWNASAETRAEVLNRAADLYEANYGELFALLTREAGKTLPDCVAELREAVDFLRYY 660
            SAATPWNASAETRAEVLNRAADLYEANYGELFALLTREAGKTLPDCVAELREAVDFLRYY
Sbjct: 601  SAATPWNASAETRAEVLNRAADLYEANYGELFALLTREAGKTLPDCVAELREAVDFLRYY 660

Query: 661  AARISAEPPVGVFTCISPWNFPLAIFSGQIAAALAVGNAVLAKPAEQTPLIAHRAISLLH 720
            AARISAEPPVGVFTCISPWNFPLAIFSGQIAAALAVGNAVLAKPAEQTPLIAHRAISLLH
Sbjct: 661  AARISAEPPVGVFTCISPWNFPLAIFSGQIAAALAVGNAVLAKPAEQTPLIAHRAISLLH 720

Query: 721  EAGVPRSALQLLPGAGAVGGALTSDARVGGVAFTGSTATALKIRAAMAEHLRPGAPLIAE 780
            EAGVPRSALQLLPGAGAVGGALTSDARVGGVAFTGSTATALKIRAAMAEHLRPGAPLIAE
Sbjct: 721  EAGVPRSALQLLPGAGAVGGALTSDARVGGVAFTGSTATALKIRAAMAEHLRPGAPLIAE 780

Query: 781  TGGLNAMIVDSTALPEQAVQSIIESAFQSAGQRCSALRCLYLQEDIADNVLKMLKGAMDA 840
            TGGLNAMIVDSTALPEQAVQSIIESAFQSAGQRCSALRCLYLQEDIADNVLKMLKGAMDA
Sbjct: 781  TGGLNAMIVDSTALPEQAVQSIIESAFQSAGQRCSALRCLYLQEDIADNVLKMLKGAMDA 840

Query: 841  LHLGDPWNLSTDSGPVIDETARAGILAHIDAARAEGRVLKEMTAPQGGTFVAPTLIEITG 900
            LHLGDPWNLSTDSGPVIDETARAGILAHIDAARAEGRVLKEMTAPQGGTFVAPTLIEITG
Sbjct: 841  LHLGDPWNLSTDSGPVIDETARAGILAHIDAARAEGRVLKEMTAPQGGTFVAPTLIEITG 900

Query: 901  IQALEQEIFGPVLHVVRFKSQDLDQIIRDINATGYGLTFGLHTRIDDRVQYICDRIHAGN 960
            IQALEQEIFGPVLHVVRFKSQDLDQIIRDINATGYGLTFGLHTRIDDRVQYICDRIHAGN
Sbjct: 901  IQALEQEIFGPVLHVVRFKSQDLDQIIRDINATGYGLTFGLHTRIDDRVQYICDRIHAGN 960

Query: 961  LYVNRNQIGAIVGSQPFGGEGLSGTGPKAGGPFYMMRFCAPDRQKSVDSWPSDAPAMTML 1020
            LYVNRNQIGAIVGSQPFGGEGLSGTGPKAGGPFYMMRFCAPDRQKSVDSWPSDAPAMTML
Sbjct: 961  LYVNRNQIGAIVGSQPFGGEGLSGTGPKAGGPFYMMRFCAPDRQKSVDSWPSDAPAMTML 1020

Query: 1021 PAPTGQPMQEITTSLPGPTGESNRLSQLARPPLLCLGPGPQAVVAQARAVHALGGTAIEA 1080
            PAPTGQPMQEITTSLPGPTGESNRLSQLARPPLLCLGPGPQAVVAQARAVHALGGTAIEA
Sbjct: 1021 PAPTGQPMQEITTSLPGPTGESNRLSQLARPPLLCLGPGPQAVVAQARAVHALGGTAIEA 1080

Query: 1081 TGPLDMRQLLTMEGTSGVIWWGDETTAREIESWLARRNGPILPLIPGLPDKARVQAERHV 1140
            TGPLDMRQLLTMEGTSGVIWWGDETTAREIESWLARRNGPILPLIPGLPDKARVQAERHV
Sbjct: 1081 TGPLDMRQLLTMEGTSGVIWWGDETTAREIESWLARRNGPILPLIPGLPDKARVQAERHV 1140

Query: 1141 CVDTTAAGGNAALLGGMG 1158
            CVDTTAAGGNAALLGGMG
Sbjct: 1141 CVDTTAAGGNAALLGGMG 1158


Lambda     K      H
   0.317    0.132    0.387 

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: 3626
Number of extensions: 133
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: 1158
Length of database: 1158
Length adjustment: 47
Effective length of query: 1111
Effective length of database: 1111
Effective search space:  1234321
Effective search space used:  1234321
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: 58 (26.9 bits)

Align candidate GFF1160 PGA1_c11750 (bifunctional protein PutA)
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.3282.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
     1e-194  633.6   0.0   1.2e-193  630.1   0.0    2.2  2  lcl|FitnessBrowser__Phaeo:GFF1160  PGA1_c11750 bifunctional protein


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF1160  PGA1_c11750 bifunctional protein PutA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  630.1   0.0  1.2e-193  1.2e-193       1     496 [.     521     999 ..     521    1002 .. 0.96
   2 !    0.7   0.0    0.0079    0.0079     238     270 ..    1093    1125 ..    1082    1146 .. 0.88

  Alignments for each domain:
  == domain 1  score: 630.1 bits;  conditional E-value: 1.2e-193
                          TIGR01238   1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgeka.kaegeaqpvknpadrkdivGqvseadaae 75 
                                        dl+   r ns G dl    +l+ +++    +  +++ a p++++ +  a    +pv+npad    vG+v++a +ae
  lcl|FitnessBrowser__Phaeo:GFF1160 521 DLFQPERPNSIGFDLGHAPTLAAIDAARAPWKSHSWAAEPLLAKAPeTATTTDEPVRNPADLT-TVGRVQTAGQAE 595
                                        789999************************************96664788899********85.79******9999 PP

                          TIGR01238  76 vqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryyakqved 151
                                        ++ a+++    ++ w+a  a+ ra +l+r+adl e +  el all reaGktl +++ae+reavdflryya ++  
  lcl|FitnessBrowser__Phaeo:GFF1160 596 IETALSA----ATPWNAS-AETRAEVLNRAADLYEANYGELFALLTREAGKTLPDCVAELREAVDFLRYYAARI-- 664
                                        8777665....568*995.899**************************************************99.. PP

                          TIGR01238 152 vldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaGvpagviqllpGrG 227
                                             +  ++G++ cispwnfplaif Gqiaaala Gn+v+akpaeqt+lia ra++ll+eaGvp +++qllpG+G
  lcl|FitnessBrowser__Phaeo:GFF1160 665 ----SAEPPVGVFTCISPWNFPLAIFSGQIAAALAVGNAVLAKPAEQTPLIAHRAISLLHEAGVPRSALQLLPGAG 736
                                        ....44579******************************************************************* PP

                          TIGR01238 228 edvGaaltsderiaGviftGstevarlinkalakredapvpliaetGGqnamivdstalaeqvvadvlasafdsaG 303
                                        + vG altsd+r++Gv+ftGst++a +i+ a+a+   + +pliaetGG namivdstal+eq v+ +++saf+saG
  lcl|FitnessBrowser__Phaeo:GFF1160 737 A-VGGALTSDARVGGVAFTGSTATALKIRAAMAEHLRPGAPLIAETGGLNAMIVDSTALPEQAVQSIIESAFQSAG 811
                                        *.************************************************************************** PP

                          TIGR01238 304 qrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkakakkvaqvkledd 379
                                        qrcsalr l++qed+ad+vl+++kGamd l++g p +l td Gpvid+ a+  +lahi++ +a ++ +++++    
  lcl|FitnessBrowser__Phaeo:GFF1160 812 QRCSALRCLYLQEDIADNVLKMLKGAMDALHLGDPWNLSTDSGPVIDETARAGILAHIDAARAEGRVLKEMTAP-- 885
                                        ******************************************************************99998765.. PP

                          TIGR01238 380 vesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrieetvrqiekrakv 455
                                           + gtfvaptl+e+  +++l++e+fGpvlhvvr+k+++ld+++  ina+Gyglt+G+h+ri++ v++i +r+++
  lcl|FitnessBrowser__Phaeo:GFF1160 886 ---QGGTFVAPTLIEITGIQALEQEIFGPVLHVVRFKSQDLDQIIRDINATGYGLTFGLHTRIDDRVQYICDRIHA 958
                                        ...59*********************************************************************** PP

                          TIGR01238 456 GnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrlt 496
                                        Gn+yvnrn++Ga+vG qpfGGeGlsGtGpkaGGp+y+ r+ 
  lcl|FitnessBrowser__Phaeo:GFF1160 959 GNLYVNRNQIGAIVGSQPFGGEGLSGTGPKAGGPFYMMRFC 999
                                        **************************************996 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.0079
                          TIGR01238  238 eriaGviftGstevarlinkalakredapvpli 270 
                                         e  +Gvi+ G   +ar i+  la+r+ +  pli
  lcl|FitnessBrowser__Phaeo:GFF1160 1093 EGTSGVIWWGDETTAREIESWLARRNGPILPLI 1125
                                         5578**********************9999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1158 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 14.50
//
[ok]

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

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

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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