Alignments for a candidate for putA in Desulfobacter vibrioformis DSM 8776

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Desulfobacter vibrioformis DSM 8776

Align Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; P5C dehydrogenase; Aldehyde dehydrogenase family 4 member A1; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_035238997.1 Q366_RS11500 L-glutamate gamma-semialdehyde dehydrogenase

Query= SwissProt::Q8CHT0
         (562 letters)



>NCBI__GCF_000745975.1:WP_035238997.1
          Length = 541

 Score =  523 bits (1347), Expect = e-153
 Identities = 260/533 (48%), Positives = 357/533 (66%), Gaps = 3/533 (0%)

Query: 30  KVTNEPILAFSQGSPERDALQKAL-KDLKGQMEAIPCVVGDEEVWTSDIQYQLSPFNHAH 88
           K  NEP+  ++ GSPER  L   L + + GQ+E IP ++  +E+ T D+   + P +H H
Sbjct: 10  KPYNEPVKTYAPGSPERRVLSAELGRQMAGQVE-IPVIINGQEIKTGDVSDVVCPHDHGH 68

Query: 89  KVAKFCYADKALLNRAIDAALAARKEWDLKPMADRAQVFLKAADMLSGPRRAEVLAKTMV 148
            +     A K  +  A+DAAL+A+  W+      RA VFLKAAD++SG   A + A TM+
Sbjct: 69  VLGHVHMAGKKEIKAAVDAALSAKSAWETMEWQARAAVFLKAADLISGKYSARLNAATML 128

Query: 149 GQGKTVIQAEIDAAAELIDFFRFNAKFAVELEGEQPISVPPSTNHTVYRGLEGFVAAISP 208
           GQ K V QAEIDA  EL+DF RFNA +  E+   QP S     N   YR LEGFV  ++P
Sbjct: 129 GQSKNVFQAEIDATCELVDFLRFNASYMEEIYANQPFSEKGVYNRLEYRPLEGFVFVLTP 188

Query: 209 FNFTAIGGNLAGAPALMGNVVLWKPSDTAMLASYAVYRILREAGLPPNIIQFVPADGPTF 268
           FNFTAI GNL   PA+MGN ++WKPS TA+L++Y + RIL+EAGLP  +I F+P  G   
Sbjct: 189 FNFTAIAGNLPTTPAMMGNAIVWKPSTTAVLSNYFLMRILKEAGLPDGVINFIPGRGSQI 248

Query: 269 GDTVTSSEHLCGINFTGSVPTFKHLWRQVAQNLDRFRTFPRLAGECGGKNFHFVHSSADV 328
           GD + + +   G++FTGS   F++LW++ AQN++ + ++PR+ GE GGK++ F H+SADV
Sbjct: 249 GDILFTHKDFAGMHFTGSTAVFQNLWKKAAQNIETYVSYPRIVGETGGKDYIFAHASADV 308

Query: 329 DSVVSGTLRSAFEYGGQKCSACSRLYVPKSLWPQIKGRLLEEHSRIKVGDPAEDFGTFFS 388
           D++V+  +R AFE+ GQKCSACSRLYVP SLWP ++ +L E+ + IKVG P  DF  F +
Sbjct: 309 DALVTAIIRGAFEFQGQKCSACSRLYVPVSLWPGVQDQLKEKIAEIKVG-PVTDFTNFVN 367

Query: 389 AVIDAKAFARIKKWLEHARSSPSLSILAGGQCNESVGYYVEPCIIESKDPQEPIMKEEIF 448
           AVID KAF  I  ++  A++S    ++ GGQ ++S GY+V P +I++K P    M +EIF
Sbjct: 368 AVIDEKAFDTIDGYISRAQASSDAEVIIGGQRDKSKGYFVHPTVIQAKTPDYESMVQEIF 427

Query: 449 GPVLTVYVYPDDKYRETLQLVDSTTSYGLTGAVFAQDKAIVQEATRMLRNAAGNFYINDK 508
           GPVLTVYVY D     TL ++D+T+ Y LTGAVFA+D++++      L + AGNFYINDK
Sbjct: 428 GPVLTVYVYEDKDLDATLDILDNTSPYALTGAVFARDRSVINALMARLTHTAGNFYINDK 487

Query: 509 STGSVVGQQPFGGARASGTNDKPGGPHYILRWTSPQVIKETHKPLGDWRYSYM 561
            TG+VVGQQPFGGAR SGTNDK G    ++RWTSP+ IKET  P  ++ Y +M
Sbjct: 488 PTGAVVGQQPFGGARKSGTNDKAGSYLNLIRWTSPRTIKETFVPSLNYHYPFM 540


Lambda     K      H
   0.319    0.135    0.411 

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: 828
Number of extensions: 31
Number of successful extensions: 2
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: 562
Length of database: 541
Length adjustment: 36
Effective length of query: 526
Effective length of database: 505
Effective search space:   265630
Effective search space used:   265630
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: 53 (25.0 bits)

Align candidate WP_035238997.1 Q366_RS11500 (L-glutamate gamma-semialdehyde dehydrogenase)
to HMM TIGR01236 (pruA: 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/TIGR01236.hmm
# target sequence database:        /tmp/gapView.3032821.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01236  [M=533]
Accession:   TIGR01236
Description: D1pyr5carbox1: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.1e-243  794.6   0.3   2.4e-243  794.5   0.3    1.0  1  NCBI__GCF_000745975.1:WP_035238997.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000745975.1:WP_035238997.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  794.5   0.3  2.4e-243  2.4e-243       2     532 ..      13     540 ..      12     541 .] 0.99

  Alignments for each domain:
  == domain 1  score: 794.5 bits;  conditional E-value: 2.4e-243
                             TIGR01236   2 nePvkefrpgskerdllrkelkelkskvleiPlviggkevvksnelievvaPadhqaklakltnateedvkka 74 
                                           nePvk ++pgs+er +l +el      ++eiP++i+g+e+ k++++ +vv P+dh ++l++++ a+++++k+a
  NCBI__GCF_000745975.1:WP_035238997.1  13 NEPVKTYAPGSPERRVLSAELGRQMAGQVEIPVIINGQEI-KTGDVSDVVCPHDHGHVLGHVHMAGKKEIKAA 84 
                                           9**********************999*************5.56668*************************** PP

                             TIGR01236  75 veaaldakkeWselpfadraaiflkaadllsgkyreeilaatmlgqsktvyqaeidavaelidffrfnvkyar 147
                                           v+aal+ak+ W++++++ raa+flkaadl+sgky + ++aatmlgqsk+v+qaeida +el+df+rfn+ y +
  NCBI__GCF_000745975.1:WP_035238997.1  85 VDAALSAKSAWETMEWQARAAVFLKAADLISGKYSARLNAATMLGQSKNVFQAEIDATCELVDFLRFNASYME 157
                                           ************************************************************************* PP

                             TIGR01236 148 elleqqPsvsapgelnkveyrpleGfvaaisPfnftaiaanlagaPalmGnvvvWkPsktavlsnyllmkile 220
                                           e+++ qP  s +g++n+ eyrpleGfv+ ++Pfnftaia+nl+++Pa+mGn++vWkPs+tavlsny lm+il+
  NCBI__GCF_000745975.1:WP_035238997.1 158 EIYANQP-FSEKGVYNRLEYRPLEGFVFVLTPFNFTAIAGNLPTTPAMMGNAIVWKPSTTAVLSNYFLMRILK 229
                                           *******.79*************************************************************** PP

                             TIGR01236 221 eaGlPpgvinfvpadgvkvsdvvladkdlaalhftGstavfkelwkkvasnldkyrnfPrivGetGGkdfvlv 293
                                           eaGlP gvinf+p+ g +++d+  ++kd+a++hftGstavf++lwkk a+n+++y ++PrivGetGGkd++++
  NCBI__GCF_000745975.1:WP_035238997.1 230 EAGLPDGVINFIPGRGSQIGDILFTHKDFAGMHFTGSTAVFQNLWKKAAQNIETYVSYPRIVGETGGKDYIFA 302
                                           ************************************************************************* PP

                             TIGR01236 294 hpsadveevvaatirgafeyqGqkcsaasrlyvpkslwkelkeellaelkkvkvgdvddlssfmgavideksf 366
                                           h+sadv+ +v+a+irgafe+qGqkcsa+srlyvp slw+ ++++l+++ +++kvg+v+d+++f+ avidek+f
  NCBI__GCF_000745975.1:WP_035238997.1 303 HASADVDALVTAIIRGAFEFQGQKCSACSRLYVPVSLWPGVQDQLKEKIAEIKVGPVTDFTNFVNAVIDEKAF 375
                                           ************************************************************************* PP

                             TIGR01236 367 akivkviekakkdpeeleilaGGkyddskGyfvePtvveskdPkeklmkeeifGPvltvyvydddkykeilev 439
                                           + i  +i +a++++ + e+++GG+ d+skGyfv+Ptv+++k P+ ++m++eifGPvltvyvy+d+  + +l++
  NCBI__GCF_000745975.1:WP_035238997.1 376 DTIDGYISRAQASS-DAEVIIGGQRDKSKGYFVHPTVIQAKTPDYESMVQEIFGPVLTVYVYEDKDLDATLDI 447
                                           ************76.99******************************************************** PP

                             TIGR01236 440 vdstskyaltGavfakdreaieeaekklrfaaGnfyindkstGavvgqqpfGGarlsGtndkaGapkillrfv 512
                                           +d+ts yaltGavfa+dr++i+    +l ++aGnfyindk+tGavvgqqpfGGar sGtndkaG+  +l+r++
  NCBI__GCF_000745975.1:WP_035238997.1 448 LDNTSPYALTGAVFARDRSVINALMARLTHTAGNFYINDKPTGAVVGQQPFGGARKSGTNDKAGSYLNLIRWT 520
                                           ************************************************************************* PP

                             TIGR01236 513 sarsiketfkeltdfkypym 532
                                           s+r+iketf++  +++yp+m
  NCBI__GCF_000745975.1:WP_035238997.1 521 SPRTIKETFVPSLNYHYPFM 540
                                           ******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (533 nodes)
Target sequences:                          1  (541 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 26.89
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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