Alignments for a candidate for astD in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for astD in Shewanella amazonensis SB2B

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate 6938906 Sama_3009 succinylglutamic semialdehyde dehydrogenase (RefSeq)

Query= reanno::SB2B:6938906
         (486 letters)



>FitnessBrowser__SB2B:6938906
          Length = 486

 Score =  968 bits (2502), Expect = 0.0
 Identities = 486/486 (100%), Positives = 486/486 (100%)

Query: 1   MTQFINGQWLAGEGKEMQSKNPANGEVIWQGKAAVPAQVQAAVMAARDAQFEWFMLGFEG 60
           MTQFINGQWLAGEGKEMQSKNPANGEVIWQGKAAVPAQVQAAVMAARDAQFEWFMLGFEG
Sbjct: 1   MTQFINGQWLAGEGKEMQSKNPANGEVIWQGKAAVPAQVQAAVMAARDAQFEWFMLGFEG 60

Query: 61  RQAIVEAYRNELEANKAELAEVIAQETGKPRWETATEAAAMIGKIGLSVSAYHKRTGTEV 120
           RQAIVEAYRNELEANKAELAEVIAQETGKPRWETATEAAAMIGKIGLSVSAYHKRTGTEV
Sbjct: 61  RQAIVEAYRNELEANKAELAEVIAQETGKPRWETATEAAAMIGKIGLSVSAYHKRTGTEV 120

Query: 121 NEGAAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKVAELM 180
           NEGAAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKVAELM
Sbjct: 121 NEGAAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKVAELM 180

Query: 181 LKLWEKAGLPAGVINLVQGEVETGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKIL 240
           LKLWEKAGLPAGVINLVQGEVETGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKIL
Sbjct: 181 LKLWEKAGLPAGVINLVQGEVETGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKIL 240

Query: 241 ALEMGGNNPLIVKGVSDTRAAIHDIIQSAFISSGQRCTCARRLYVEKGAEGDKLLAGLVE 300
           ALEMGGNNPLIVKGVSDTRAAIHDIIQSAFISSGQRCTCARRLYVEKGAEGDKLLAGLVE
Sbjct: 241 ALEMGGNNPLIVKGVSDTRAAIHDIIQSAFISSGQRCTCARRLYVEKGAEGDKLLAGLVE 300

Query: 301 AVKAIKVGPWNADPQPFMGSMISETAAKGMLDAQRNLLNLGAKSLVEMTHLQAGTGLVSP 360
           AVKAIKVGPWNADPQPFMGSMISETAAKGMLDAQRNLLNLGAKSLVEMTHLQAGTGLVSP
Sbjct: 301 AVKAIKVGPWNADPQPFMGSMISETAAKGMLDAQRNLLNLGAKSLVEMTHLQAGTGLVSP 360

Query: 361 GLIDVTEVIELPDEEYFGPLLQVVRYTSFDEAIRLANDTRYGLSAGILADDKADYEYFLA 420
           GLIDVTEVIELPDEEYFGPLLQVVRYTSFDEAIRLANDTRYGLSAGILADDKADYEYFLA
Sbjct: 361 GLIDVTEVIELPDEEYFGPLLQVVRYTSFDEAIRLANDTRYGLSAGILADDKADYEYFLA 420

Query: 421 RIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASMEADSVTLPASL 480
           RIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASMEADSVTLPASL
Sbjct: 421 RIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASMEADSVTLPASL 480

Query: 481 SPGLTL 486
           SPGLTL
Sbjct: 481 SPGLTL 486


Lambda     K      H
   0.317    0.133    0.393 

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: 969
Number of extensions: 21
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: 486
Length of database: 486
Length adjustment: 34
Effective length of query: 452
Effective length of database: 452
Effective search space:   204304
Effective search space used:   204304
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: 52 (24.6 bits)

Align candidate 6938906 Sama_3009 (succinylglutamic semialdehyde dehydrogenase (RefSeq))
to HMM TIGR03240 (astD: succinylglutamate-semialdehyde dehydrogenase (EC 1.2.1.71))

# 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/TIGR03240.hmm
# target sequence database:        /tmp/gapView.13992.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03240  [M=484]
Accession:   TIGR03240
Description: arg_catab_astD: succinylglutamate-semialdehyde 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-248  810.7   1.6   2.4e-248  810.6   1.6    1.0  1  lcl|FitnessBrowser__SB2B:6938906  Sama_3009 succinylglutamic semia


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6938906  Sama_3009 succinylglutamic semialdehyde dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  810.6   1.6  2.4e-248  2.4e-248       1     483 [.       3     485 ..       3     486 .] 1.00

  Alignments for each domain:
  == domain 1  score: 810.6 bits;  conditional E-value: 2.4e-248
                         TIGR03240   1 lfidGkwraGqGeslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaelleeekeel 77 
                                       +fi+G+w aG+G++++s++p+++ev+wqgkaa  aqv++av aar+a  +w  l +e r+a+v+ + + le +k+el
  lcl|FitnessBrowser__SB2B:6938906   3 QFINGQWLAGEGKEMQSKNPANGEVIWQGKAAVPAQVQAAVMAARDAQFEWFMLGFEGRQAIVEAYRNELEANKAEL 79 
                                       69*************************************************************************** PP

                         TIGR03240  78 aeviaketgkplweartevasmvakvaisikayeertGekeseladakavlrhrphGvlavfGpynfpGhlpnGhiv 154
                                       aevia+etgkp+we++te a+m++k+ +s+ ay++rtG++ +e a+++avlrh+phGv+avfGpynfpGhlpnGhiv
  lcl|FitnessBrowser__SB2B:6938906  80 AEVIAQETGKPRWETATEAAAMIGKIGLSVSAYHKRTGTEVNEGAAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIV 156
                                       ***************************************************************************** PP

                         TIGR03240 155 pallaGntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeedidGllftGssntGallhrqla 231
                                       pallaGntvvfkpseltp+vae ++klwekaGlpaGv+nlvqG++etGkala+++++dGl+ftGss+tG+llh+q+a
  lcl|FitnessBrowser__SB2B:6938906 157 PALLAGNTVVFKPSELTPKVAELMLKLWEKAGLPAGVINLVQGEVETGKALASHPQLDGLFFTGSSRTGHLLHQQYA 233
                                       ***************************************************************************** PP

                         TIGR03240 232 grpekilalelGGnnplvveevkdidaavhlivqsafisaGqrctcarrllvkdgaeGdallerlvevaerltvgky 308
                                       g+p kilale+GGnnpl+v+ v+d+ aa+h+i+qsafis+Gqrctcarrl v++gaeGd+ll+ lve  ++++vg +
  lcl|FitnessBrowser__SB2B:6938906 234 GHPGKILALEMGGNNPLIVKGVSDTRAAIHDIIQSAFISSGQRCTCARRLYVEKGAEGDKLLAGLVEAVKAIKVGPW 310
                                       ***************************************************************************** PP

                         TIGR03240 309 daepqpflGavisekaakellaaqekllalggksllelkqleeeaalltpgiidvtevaevpdeeyfgpllkvlryk 385
                                       +a+pqpf+G++ise aak +l+aq++ll+lg+ksl+e+++l+++++l++pg+idvtev e+pdeeyfgpll+v+ry+
  lcl|FitnessBrowser__SB2B:6938906 311 NADPQPFMGSMISETAAKGMLDAQRNLLNLGAKSLVEMTHLQAGTGLVSPGLIDVTEVIELPDEEYFGPLLQVVRYT 387
                                       ***************************************************************************** PP

                         TIGR03240 386 dfdealaeanntrfGlaaGllsddrelydkflleiraGivnwnkpltGassaapfGGiGasGnhrpsayyaadycay 462
                                       +fdea++ an+tr+Gl+aG+l+dd++ y++fl +iraGivnwnk++tGas+aapfGG+GasGnhr+sa+yaadycay
  lcl|FitnessBrowser__SB2B:6938906 388 SFDEAIRLANDTRYGLSAGILADDKADYEYFLARIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAY 464
                                       ***************************************************************************** PP

                         TIGR03240 463 pvasleadslalpatlspGlk 483
                                       pvas+eads++lpa+lspGl+
  lcl|FitnessBrowser__SB2B:6938906 465 PVASMEADSVTLPASLSPGLT 485
                                       *******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (484 nodes)
Target sequences:                          1  (486 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 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.66
//
[ok]

This GapMind analysis is from Sep 17 2021. 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 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