Alignments for a candidate for astD in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for astD in Shewanella oneidensis MR-1

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate 199807 SO0619 succinylglutamic semialdehyde dehydrogenase (NCBI ptt file)

Query= reanno::MR1:199807
         (487 letters)



>FitnessBrowser__MR1:199807
          Length = 487

 Score =  970 bits (2508), Expect = 0.0
 Identities = 487/487 (100%), Positives = 487/487 (100%)

Query: 1   MTHFIKGQWHTGKGHDVASSNPANGEIIWRGQTATAEQVNAAVDAAREAQFDWFILGFDA 60
           MTHFIKGQWHTGKGHDVASSNPANGEIIWRGQTATAEQVNAAVDAAREAQFDWFILGFDA
Sbjct: 1   MTHFIKGQWHTGKGHDVASSNPANGEIIWRGQTATAEQVNAAVDAAREAQFDWFILGFDA 60

Query: 61  RLKIVEAYRSQLEANKAELAETIAQETGKPQWETATEVAAMIGKIGLSASAYNKRTGTET 120
           RLKIVEAYRSQLEANKAELAETIAQETGKPQWETATEVAAMIGKIGLSASAYNKRTGTET
Sbjct: 61  RLKIVEAYRSQLEANKAELAETIAQETGKPQWETATEVAAMIGKIGLSASAYNKRTGTET 120

Query: 121 NDTPAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVVFKPSELTPKVAELM 180
           NDTPAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVVFKPSELTPKVAELM
Sbjct: 121 NDTPAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVVFKPSELTPKVAELM 180

Query: 181 VTLWEKSGLPAGVLNLVQGEVDTGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKIL 240
           VTLWEKSGLPAGVLNLVQGEVDTGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKIL
Sbjct: 181 VTLWEKSGLPAGVLNLVQGEVDTGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKIL 240

Query: 241 ALEMGGNNPLIIKGVADIKAAVHDILQSAYISSGQRCTCARRLYVEQGEQGDALVAKLVE 300
           ALEMGGNNPLIIKGVADIKAAVHDILQSAYISSGQRCTCARRLYVEQGEQGDALVAKLVE
Sbjct: 241 ALEMGGNNPLIIKGVADIKAAVHDILQSAYISSGQRCTCARRLYVEQGEQGDALVAKLVE 300

Query: 301 AVKQIKVGPWNAQPQPFMGSMISEAAAKGMVAAQANLLSLGGVPLVELMHLQAGTGLVSP 360
           AVKQIKVGPWNAQPQPFMGSMISEAAAKGMVAAQANLLSLGGVPLVELMHLQAGTGLVSP
Sbjct: 301 AVKQIKVGPWNAQPQPFMGSMISEAAAKGMVAAQANLLSLGGVPLVELMHLQAGTGLVSP 360

Query: 361 GLIDVTAVSELPDEEYFGPLLQLVRYSDFDQAIKLANQTRYGLSAGILADSREDYEYFLA 420
           GLIDVTAVSELPDEEYFGPLLQLVRYSDFDQAIKLANQTRYGLSAGILADSREDYEYFLA
Sbjct: 361 GLIDVTAVSELPDEEYFGPLLQLVRYSDFDQAIKLANQTRYGLSAGILADSREDYEYFLA 420

Query: 421 RIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASVEADAVSLPATL 480
           RIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASVEADAVSLPATL
Sbjct: 421 RIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASVEADAVSLPATL 480

Query: 481 SPGLTLS 487
           SPGLTLS
Sbjct: 481 SPGLTLS 487


Lambda     K      H
   0.316    0.133    0.391 

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: 1049
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: 487
Length of database: 487
Length adjustment: 34
Effective length of query: 453
Effective length of database: 453
Effective search space:   205209
Effective search space used:   205209
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 199807 SO0619 (succinylglutamic semialdehyde dehydrogenase (NCBI ptt file))
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.26065.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   8.2e-248  808.8   1.6   9.3e-248  808.6   1.6    1.0  1  lcl|FitnessBrowser__MR1:199807  SO0619 succinylglutamic semialde


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:199807  SO0619 succinylglutamic semialdehyde dehydrogenase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  808.6   1.6  9.3e-248  9.3e-248       1     483 [.       3     485 ..       3     486 .. 1.00

  Alignments for each domain:
  == domain 1  score: 808.6 bits;  conditional E-value: 9.3e-248
                       TIGR03240   1 lfidGkwraGqGeslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaelleeekeelae 79 
                                     +fi+G+w++G+G++++s++p+++e +w+g++a+a+qv++av aar+a  +w  l +++r+++v+ + ++le +k+elae
  lcl|FitnessBrowser__MR1:199807   3 HFIKGQWHTGKGHDVASSNPANGEIIWRGQTATAEQVNAAVDAAREAQFDWFILGFDARLKIVEAYRSQLEANKAELAE 81 
                                     69***************************************************************************** PP

                       TIGR03240  80 viaketgkplweartevasmvakvaisikayeertGekeseladakavlrhrphGvlavfGpynfpGhlpnGhivpall 158
                                     +ia+etgkp+we++teva+m++k+ +s  ay++rtG++ +++++++avlrh+phGv+avfGpynfpGhlpnGhivpall
  lcl|FitnessBrowser__MR1:199807  82 TIAQETGKPQWETATEVAAMIGKIGLSASAYNKRTGTETNDTPAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALL 160
                                     ******************************************************************************* PP

                       TIGR03240 159 aGntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeedidGllftGssntGallhrqlagrpeki 237
                                     aGn+vvfkpseltp+vae +v lwek+GlpaGvlnlvqG+++tGkala+++++dGl+ftGss+tG+llh+q+ag+p ki
  lcl|FitnessBrowser__MR1:199807 161 AGNSVVFKPSELTPKVAELMVTLWEKSGLPAGVLNLVQGEVDTGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKI 239
                                     ******************************************************************************* PP

                       TIGR03240 238 lalelGGnnplvveevkdidaavhlivqsafisaGqrctcarrllvkdgaeGdallerlvevaerltvgkydaepqpfl 316
                                     lale+GGnnpl+++ v+di+aavh+i+qsa+is+Gqrctcarrl v++g++Gdal+++lve  ++++vg ++a+pqpf+
  lcl|FitnessBrowser__MR1:199807 240 LALEMGGNNPLIIKGVADIKAAVHDILQSAYISSGQRCTCARRLYVEQGEQGDALVAKLVEAVKQIKVGPWNAQPQPFM 318
                                     ******************************************************************************* PP

                       TIGR03240 317 Gavisekaakellaaqekllalggksllelkqleeeaalltpgiidvtevaevpdeeyfgpllkvlrykdfdealaean 395
                                     G++ise aak ++aaq++ll lgg  l+el +l+++++l++pg+idvt+v+e+pdeeyfgpll+++ry+dfd+a++ an
  lcl|FitnessBrowser__MR1:199807 319 GSMISEAAAKGMVAAQANLLSLGGVPLVELMHLQAGTGLVSPGLIDVTAVSELPDEEYFGPLLQLVRYSDFDQAIKLAN 397
                                     ******************************************************************************* PP

                       TIGR03240 396 ntrfGlaaGllsddrelydkflleiraGivnwnkpltGassaapfGGiGasGnhrpsayyaadycaypvasleadslal 474
                                     +tr+Gl+aG+l+d+re y++fl +iraGivnwnk++tGas+aapfGG+GasGnhr+sa+yaadycaypvas+ead ++l
  lcl|FitnessBrowser__MR1:199807 398 QTRYGLSAGILADSREDYEYFLARIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASVEADAVSL 476
                                     ******************************************************************************* PP

                       TIGR03240 475 patlspGlk 483
                                     patlspGl+
  lcl|FitnessBrowser__MR1:199807 477 PATLSPGLT 485
                                     *******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (484 nodes)
Target sequences:                          1  (487 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: 00:00:00.02
# Mc/sec: 11.29
//
[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