Alignments for a candidate for rocA in Desulfacinum infernum DSM 9756

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocA in Desulfacinum infernum DSM 9756

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_073040272.1 BUB04_RS13170 L-glutamate gamma-semialdehyde dehydrogenase

Query= BRENDA::Q9K9B2
         (515 letters)



>NCBI__GCF_900129305.1:WP_073040272.1
          Length = 995

 Score =  508 bits (1309), Expect = e-148
 Identities = 252/510 (49%), Positives = 341/510 (66%)

Query: 4   PYKHEPFTDFTVEANRKAFEEALGLVEKELGKEYPLIINGERVTTEDKIQSWNPARKDQL 63
           P+ +EP  D+T+   R+ FE  L  + K+   + PL+ING++V T +   S NP R DQ+
Sbjct: 474 PFVNEPPWDWTIAEVRRTFERTLAKLPKDFPVQVPLVINGKKVRTRETFSSTNPNRTDQV 533

Query: 64  VGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERANILVKAAAIIRRRKHEFSAWLVHEA 123
           VG V+ A ++ A +A+ +A +AF  WR+  P ERA  L +AA   R R++E +A  V+E 
Sbjct: 534 VGVVASAGEEEALQAVAAAKDAFDAWRDTPPRERAEYLFRAAQAARNRRYELAALQVYEV 593

Query: 124 GKPWKEADADTAEAIDFLEYYARQMIELNRGKEILSRPGEQNRYFYTPMGVTVTISPWNF 183
           GK WKEADAD  EAIDFLEYY R+MI L   + +   PGE +  FY P GVT  ++PWNF
Sbjct: 594 GKSWKEADADVCEAIDFLEYYGREMIRLGTPRRMGHVPGEVSHLFYEPRGVTAVVAPWNF 653

Query: 184 ALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFVEVLEDAGLPKGVINYVPGSGAEVGD 243
             AI VG   A +VTGNTVV KPAS +PV+      + E+A LPKGV+N++PG G ++GD
Sbjct: 654 PFAISVGMTSAALVTGNTVVYKPASQSPVIGYWVYRIFEEAKLPKGVLNFLPGPGGKIGD 713

Query: 244 YLVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKDTVVVDRDADLDL 303
            LV HP  ++I FTGSK++G+R+ ERAA        +K V+ EMGGK+ +++D DADLD 
Sbjct: 714 LLVTHPDVAMIAFTGSKEIGLRIIERAARTPSDAQFVKNVVAEMGGKNAIIIDADADLDE 773

Query: 304 AAESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNLTVGDPTNRDNYMGPVI 363
           A   +L SAFG+ GQKCSA SR ++ ++ YD++LE+  A A++L +G   N  N MG VI
Sbjct: 774 AVVQVLHSAFGYQGQKCSACSRLIVLEENYDKLLERLRAAAESLELGPVENPKNVMGAVI 833

Query: 364 DEKAFEKIMSYIEIGKKEGRLMTGGEGDSSTGFFIQPTIIADLDPEAVIMQEEIFGPVVA 423
           D +A EKI+ YIEIGK+EG+++     +   G F+   I  ++ PE  + QEEIFGPV++
Sbjct: 834 DARAREKILEYIEIGKREGKVLVERPVEGKNGHFVPLAIFTEIRPEHRLAQEEIFGPVLS 893

Query: 424 FSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGNLYFNRNCTGAIVGYHP 483
             K  DFD ALE+AN+T+Y LTGAV +R+  +IE+A+R F VGNLY NR  TGAIV  HP
Sbjct: 894 VLKVRDFDEALEVANSTQYALTGAVFSRSPENIEKARRRFRVGNLYINRGSTGAIVERHP 953

Query: 484 FGGFKMSGTDSKAGGPDYLALHMQAKTVSE 513
           FGGFKMSG  SKAGGPDYL   M  + V+E
Sbjct: 954 FGGFKMSGVGSKAGGPDYLLQFMVPRNVAE 983


Lambda     K      H
   0.316    0.134    0.388 

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: 1212
Number of extensions: 47
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: 515
Length of database: 995
Length adjustment: 39
Effective length of query: 476
Effective length of database: 956
Effective search space:   455056
Effective search space used:   455056
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 (21.6 bits)
S2: 55 (25.8 bits)

Align candidate WP_073040272.1 BUB04_RS13170 (L-glutamate gamma-semialdehyde dehydrogenase)
to HMM TIGR01237 (pruA: putative 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/TIGR01237.hmm
# target sequence database:        /tmp/gapView.22278.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01237  [M=511]
Accession:   TIGR01237
Description: D1pyr5carbox2: putative 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-202  660.2   0.0   1.5e-202  659.9   0.0    1.1  1  lcl|NCBI__GCF_900129305.1:WP_073040272.1  BUB04_RS13170 L-glutamate gamma-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900129305.1:WP_073040272.1  BUB04_RS13170 L-glutamate gamma-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  659.9   0.0  1.5e-202  1.5e-202       3     510 ..     477     984 ..     475     985 .. 0.99

  Alignments for each domain:
  == domain 1  score: 659.9 bits;  conditional E-value: 1.5e-202
                                 TIGR01237   3 nepftdfadeelvqafkkalakvkellGkdyplvinGeeveteakidsinpadksevvGkvakasveda 71 
                                               nep  d++ +e +++f+++lak+ + +  + plvinG++v t +  +s np ++++vvG va a  e+a
  lcl|NCBI__GCF_900129305.1:WP_073040272.1 477 NEPPWDWTIAEVRRTFERTLAKLPKDFPVQVPLVINGKKVRTRETFSSTNPNRTDQVVGVVASAGEEEA 545
                                               78999******************999******************************************* PP

                                 TIGR01237  72 eqalqaakkafeewkktdveeraaillkaaailkrrrhelsallvlevGkiyaeadaevaeaidfleyy 140
                                                qa+ aak af++w+ t+++era+ l++aa+  ++rr+el+al v evGk+++eada+v+eaidfleyy
  lcl|NCBI__GCF_900129305.1:WP_073040272.1 546 LQAVAAAKDAFDAWRDTPPRERAEYLFRAAQAARNRRYELAALQVYEVGKSWKEADADVCEAIDFLEYY 614
                                               ********************************************************************* PP

                                 TIGR01237 141 aremiklakskevlsieGeknrylyiplGvavvispwnfplailvGmtvapivtGncvvlkpaeaatvi 209
                                                remi+l   +   +++Ge  +++y p+Gv+ v++pwnfp+ai vGmt a++vtGn+vv kpa++++vi
  lcl|NCBI__GCF_900129305.1:WP_073040272.1 615 GREMIRLGTPRRMGHVPGEVSHLFYEPRGVTAVVAPWNFPFAISVGMTSAALVTGNTVVYKPASQSPVI 683
                                               ********************************************************************* PP

                                 TIGR01237 210 aaklveileeaGlpkGvlqfvpGkGsevGeylvdhpktrlitftGsrevGlriyedaakvqpGqkhlkr 278
                                                  +  i+eea lpkGvl+f+pG G ++G+ lv+hp++ +i+ftGs+e+Glri e+aa+     +++k 
  lcl|NCBI__GCF_900129305.1:WP_073040272.1 684 GYWVYRIFEEAKLPKGVLNFLPGPGGKIGDLLVTHPDVAMIAFTGSKEIGLRIIERAARTPSDAQFVKN 752
                                               ********************************************************************* PP

                                 TIGR01237 279 viaelGGkdavivdesadieqavaaavtsafGfaGqkcsaasrvvvlekvydevverfveatkslkvgk 347
                                               v+ae+GGk+a+i+d +ad+++av  +++safG++Gqkcsa+sr++vle+ yd+++er+  a++sl++g+
  lcl|NCBI__GCF_900129305.1:WP_073040272.1 753 VVAEMGGKNAIIIDADADLDEAVVQVLHSAFGYQGQKCSACSRLIVLEENYDKLLERLRAAAESLELGP 821
                                               ********************************************************************* PP

                                 TIGR01237 348 tdeadvqvgpvidqksfdkikeyielgkaegklvlggedddskGyfikptifkdvdrkarlaqeeifGp 416
                                                ++++  +g+vid+++ +ki eyie+gk egk+++    ++++G+f+  +if+++ ++ rlaqeeifGp
  lcl|NCBI__GCF_900129305.1:WP_073040272.1 822 VENPKNVMGAVIDARAREKILEYIEIGKREGKVLVERPVEGKNGHFVPLAIFTEIRPEHRLAQEEIFGP 890
                                               ********************************************************************* PP

                                 TIGR01237 417 vvavlrakdfdealeiansteygltGgvisnsrerierakaefevGnlyfnrkitGaivgvqpfGGfkm 485
                                               v++vl+++dfdeale+anst+y+ltG+v+s+s+e+ie+a+  f+vGnly+nr  tGaiv ++pfGGfkm
  lcl|NCBI__GCF_900129305.1:WP_073040272.1 891 VLSVLKVRDFDEALEVANSTQYALTGAVFSRSPENIEKARRRFRVGNLYINRGSTGAIVERHPFGGFKM 959
                                               ********************************************************************* PP

                                 TIGR01237 486 sGtdskaGGpdylaqflqaktvter 510
                                               sG++skaGGpdyl+qf+ +++v+e+
  lcl|NCBI__GCF_900129305.1:WP_073040272.1 960 SGVGSKAGGPDYLLQFMVPRNVAEN 984
                                               ***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (511 nodes)
Target sequences:                          1  (995 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: 00:00:00.04
# Mc/sec: 12.43
//
[ok]

This GapMind analysis is from Sep 24 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