Alignments for a candidate for astD in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for astD in Shewanella loihica PV-4

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate 5208068 Shew_0580 succinylglutamic semialdehyde dehydrogenase (RefSeq)

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



>FitnessBrowser__PV4:5208068
          Length = 487

 Score =  857 bits (2215), Expect = 0.0
 Identities = 418/486 (86%), Positives = 451/486 (92%)

Query: 1   MTHFIKGQWHTGKGHDVASSNPANGEIIWRGQTATAEQVNAAVDAAREAQFDWFILGFDA 60
           M+ FI GQW  G GHDV S NPAN E+IW  +TAT EQVNAAV+AAR AQFDWF+LGFDA
Sbjct: 2   MSQFINGQWVAGLGHDVVSKNPANQEVIWESKTATPEQVNAAVEAARAAQFDWFMLGFDA 61

Query: 61  RLKIVEAYRSQLEANKAELAETIAQETGKPQWETATEVAAMIGKIGLSASAYNKRTGTET 120
           RL IVEAYR QLEA+K ++AE IAQETGKPQWETATE  AMIGKIGLS +AY+KRTGT  
Sbjct: 62  RLAIVEAYRDQLEAHKGDIAEVIAQETGKPQWETATEAGAMIGKIGLSVAAYHKRTGTSE 121

Query: 121 NDTPAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVVFKPSELTPKVAELM 180
           NDTPAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGN+VVFKPSELTPK AELM
Sbjct: 122 NDTPAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKTAELM 181

Query: 181 VTLWEKSGLPAGVLNLVQGEVDTGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKIL 240
           + LWEK+GLPAGV+NLVQGEV+TGKALASHPQ+DGLFFTGSSRTGH+LHQQYAGHPGKIL
Sbjct: 182 LKLWEKAGLPAGVINLVQGEVETGKALASHPQIDGLFFTGSSRTGHILHQQYAGHPGKIL 241

Query: 241 ALEMGGNNPLIIKGVADIKAAVHDILQSAYISSGQRCTCARRLYVEQGEQGDALVAKLVE 300
           ALEMGGNNPLIIKGV D  AAVHDI+QSAYISSGQRCTCARRLYVE+G +GDAL+AKL E
Sbjct: 242 ALEMGGNNPLIIKGVKDTLAAVHDIIQSAYISSGQRCTCARRLYVEKGAEGDALLAKLAE 301

Query: 301 AVKQIKVGPWNAQPQPFMGSMISEAAAKGMVAAQANLLSLGGVPLVELMHLQAGTGLVSP 360
           AVKQIKVGPWNAQPQPFMGSMISEAAAKGMV AQ NL++LGG PLVEL HL+AGTGLVSP
Sbjct: 302 AVKQIKVGPWNAQPQPFMGSMISEAAAKGMVEAQRNLINLGGTPLVELKHLEAGTGLVSP 361

Query: 361 GLIDVTAVSELPDEEYFGPLLQLVRYSDFDQAIKLANQTRYGLSAGILADSREDYEYFLA 420
           GLIDVT V ELPDEEYFGPLLQ+VRY+DFD+AIKLAN TRYGLSAGILADSREDY+YFLA
Sbjct: 362 GLIDVTQVIELPDEEYFGPLLQVVRYTDFDEAIKLANDTRYGLSAGILADSREDYDYFLA 421

Query: 421 RIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASVEADAVSLPATL 480
           RIRAGIVNWNKQITGASG+APFGGVGASGNHRASAFYAADYCAYPVASVEADA+++PA+L
Sbjct: 422 RIRAGIVNWNKQITGASGSAPFGGVGASGNHRASAFYAADYCAYPVASVEADALAMPASL 481

Query: 481 SPGLTL 486
           SPGLTL
Sbjct: 482 SPGLTL 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: 985
Number of extensions: 29
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 5208068 Shew_0580 (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.4186.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   5.4e-249  812.7   1.0   6.1e-249  812.5   1.0    1.0  1  lcl|FitnessBrowser__PV4:5208068  Shew_0580 succinylglutamic semia


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208068  Shew_0580 succinylglutamic semialdehyde dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  812.5   1.0  6.1e-249  6.1e-249       1     483 [.       4     486 ..       4     487 .] 1.00

  Alignments for each domain:
  == domain 1  score: 812.5 bits;  conditional E-value: 6.1e-249
                        TIGR03240   1 lfidGkwraGqGeslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaelleeekeela 78 
                                      +fi+G+w aG G+++ s++p++qev+w++k+a+ +qv++av+aar+a  +w  l +++r+a+v+ + ++le +k ++a
  lcl|FitnessBrowser__PV4:5208068   4 QFINGQWVAGLGHDVVSKNPANQEVIWESKTATPEQVNAAVEAARAAQFDWFMLGFDARLAIVEAYRDQLEAHKGDIA 81 
                                      69**************************************************************************** PP

                        TIGR03240  79 eviaketgkplweartevasmvakvaisikayeertGekeseladakavlrhrphGvlavfGpynfpGhlpnGhivpa 156
                                      evia+etgkp+we++te ++m++k+ +s+ ay++rtG++e+++++++avlrh+phGv+avfGpynfpGhlpnGhivpa
  lcl|FitnessBrowser__PV4:5208068  82 EVIAQETGKPQWETATEAGAMIGKIGLSVAAYHKRTGTSENDTPAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPA 159
                                      ****************************************************************************** PP

                        TIGR03240 157 llaGntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeedidGllftGssntGallhrqlagrp 234
                                      llaGntvvfkpseltp++ae ++klwekaGlpaGv+nlvqG++etGkala++++idGl+ftGss+tG++lh+q+ag+p
  lcl|FitnessBrowser__PV4:5208068 160 LLAGNTVVFKPSELTPKTAELMLKLWEKAGLPAGVINLVQGEVETGKALASHPQIDGLFFTGSSRTGHILHQQYAGHP 237
                                      ****************************************************************************** PP

                        TIGR03240 235 ekilalelGGnnplvveevkdidaavhlivqsafisaGqrctcarrllvkdgaeGdallerlvevaerltvgkydaep 312
                                       kilale+GGnnpl+++ vkd+ aavh+i+qsa+is+Gqrctcarrl v++gaeGdall++l e  ++++vg ++a+p
  lcl|FitnessBrowser__PV4:5208068 238 GKILALEMGGNNPLIIKGVKDTLAAVHDIIQSAYISSGQRCTCARRLYVEKGAEGDALLAKLAEAVKQIKVGPWNAQP 315
                                      ****************************************************************************** PP

                        TIGR03240 313 qpflGavisekaakellaaqekllalggksllelkqleeeaalltpgiidvtevaevpdeeyfgpllkvlrykdfdea 390
                                      qpf+G++ise aak +++aq++l +lgg+ l+elk+le++++l++pg+idvt+v e+pdeeyfgpll+v+ry+dfdea
  lcl|FitnessBrowser__PV4:5208068 316 QPFMGSMISEAAAKGMVEAQRNLINLGGTPLVELKHLEAGTGLVSPGLIDVTQVIELPDEEYFGPLLQVVRYTDFDEA 393
                                      ****************************************************************************** PP

                        TIGR03240 391 laeanntrfGlaaGllsddrelydkflleiraGivnwnkpltGassaapfGGiGasGnhrpsayyaadycaypvasle 468
                                      ++ an+tr+Gl+aG+l+d+re yd+fl +iraGivnwnk++tGas++apfGG+GasGnhr+sa+yaadycaypvas+e
  lcl|FitnessBrowser__PV4:5208068 394 IKLANDTRYGLSAGILADSREDYDYFLARIRAGIVNWNKQITGASGSAPFGGVGASGNHRASAFYAADYCAYPVASVE 471
                                      ****************************************************************************** PP

                        TIGR03240 469 adslalpatlspGlk 483
                                      ad la+pa+lspGl+
  lcl|FitnessBrowser__PV4:5208068 472 ADALAMPASLSPGLT 486
                                      *************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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.84
//
[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