GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Shewanella sp. ANA-3

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate 7023382 Shewana3_0612 succinylglutamic semialdehyde dehydrogenase (RefSeq)

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



>FitnessBrowser__ANA3:7023382
          Length = 487

 Score =  935 bits (2416), Expect = 0.0
 Identities = 466/486 (95%), Positives = 476/486 (97%)

Query: 1   MTHFIKGQWHTGKGHDVASSNPANGEIIWRGQTATAEQVNAAVDAAREAQFDWFILGFDA 60
           MTHFIKGQW  GKGHDV SSNPAN EIIWRGQTATAEQVNAAVDAAREAQFDWF+LGFD 
Sbjct: 1   MTHFIKGQWQAGKGHDVTSSNPANSEIIWRGQTATAEQVNAAVDAAREAQFDWFMLGFDG 60

Query: 61  RLKIVEAYRSQLEANKAELAETIAQETGKPQWETATEVAAMIGKIGLSASAYNKRTGTET 120
           RLKIVEAYRSQLEANKAELAETIAQETGKPQWETATEVAAMIGKIGLSA+AYNKRTGTE 
Sbjct: 61  RLKIVEAYRSQLEANKAELAETIAQETGKPQWETATEVAAMIGKIGLSATAYNKRTGTEA 120

Query: 121 NDTPAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVVFKPSELTPKVAELM 180
           NDTPAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGN+VVFKPSELTPKVAELM
Sbjct: 121 NDTPAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKVAELM 180

Query: 181 VTLWEKSGLPAGVLNLVQGEVDTGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKIL 240
           V+LWEK+GLPAGV+NLVQGEVDTGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKIL
Sbjct: 181 VSLWEKAGLPAGVINLVQGEVDTGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKIL 240

Query: 241 ALEMGGNNPLIIKGVADIKAAVHDILQSAYISSGQRCTCARRLYVEQGEQGDALVAKLVE 300
           ALEMGGNNPLIIKGVADIKAAVHDILQSAYISSGQRCTCARRLYVEQGEQGDALVAKLVE
Sbjct: 241 ALEMGGNNPLIIKGVADIKAAVHDILQSAYISSGQRCTCARRLYVEQGEQGDALVAKLVE 300

Query: 301 AVKQIKVGPWNAQPQPFMGSMISEAAAKGMVAAQANLLSLGGVPLVELMHLQAGTGLVSP 360
           AVKQIKVGPWNAQPQPFMGSMISEAAAKGMVAAQANL +LGGV LVEL HLQAGTGLVSP
Sbjct: 301 AVKQIKVGPWNAQPQPFMGSMISEAAAKGMVAAQANLQNLGGVSLVELSHLQAGTGLVSP 360

Query: 361 GLIDVTAVSELPDEEYFGPLLQLVRYSDFDQAIKLANQTRYGLSAGILADSREDYEYFLA 420
           GLIDVTAV ELPDEEYFGPLLQLVRYSDFDQAIKLANQTRYGLSAGILADSR+DYEYFLA
Sbjct: 361 GLIDVTAVGELPDEEYFGPLLQLVRYSDFDQAIKLANQTRYGLSAGILADSRDDYEYFLA 420

Query: 421 RIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASVEADAVSLPATL 480
           RIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASVEADAVSLPA+L
Sbjct: 421 RIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASVEADAVSLPASL 480

Query: 481 SPGLTL 486
           SPGL+L
Sbjct: 481 SPGLSL 486


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: 1026
Number of extensions: 28
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 7023382 Shewana3_0612 (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.2618581.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   9.5e-249  811.9   2.4   1.1e-248  811.7   2.4    1.0  1  lcl|FitnessBrowser__ANA3:7023382  Shewana3_0612 succinylglutamic s


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7023382  Shewana3_0612 succinylglutamic semialdehyde dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  811.7   2.4  1.1e-248  1.1e-248       1     483 [.       3     485 ..       3     486 .. 1.00

  Alignments for each domain:
  == domain 1  score: 811.7 bits;  conditional E-value: 1.1e-248
                         TIGR03240   1 lfidGkwraGqGeslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaelleeekeel 77 
                                       +fi+G+w+aG+G++++s++p+++e +w+g++a+a+qv++av aar+a  +w  l ++ r+++v+ + ++le +k+el
  lcl|FitnessBrowser__ANA3:7023382   3 HFIKGQWQAGKGHDVTSSNPANSEIIWRGQTATAEQVNAAVDAAREAQFDWFMLGFDGRLKIVEAYRSQLEANKAEL 79 
                                       69*************************************************************************** PP

                         TIGR03240  78 aeviaketgkplweartevasmvakvaisikayeertGekeseladakavlrhrphGvlavfGpynfpGhlpnGhiv 154
                                       ae+ia+etgkp+we++teva+m++k+ +s  ay++rtG++++++++++avlrh+phGv+avfGpynfpGhlpnGhiv
  lcl|FitnessBrowser__ANA3:7023382  80 AETIAQETGKPQWETATEVAAMIGKIGLSATAYNKRTGTEANDTPAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIV 156
                                       ***************************************************************************** PP

                         TIGR03240 155 pallaGntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeedidGllftGssntGallhrqla 231
                                       pallaGntvvfkpseltp+vae +v lwekaGlpaGv+nlvqG+++tGkala+++++dGl+ftGss+tG+llh+q+a
  lcl|FitnessBrowser__ANA3:7023382 157 PALLAGNTVVFKPSELTPKVAELMVSLWEKAGLPAGVINLVQGEVDTGKALASHPQLDGLFFTGSSRTGHLLHQQYA 233
                                       ***************************************************************************** PP

                         TIGR03240 232 grpekilalelGGnnplvveevkdidaavhlivqsafisaGqrctcarrllvkdgaeGdallerlvevaerltvgky 308
                                       g+p kilale+GGnnpl+++ v+di+aavh+i+qsa+is+Gqrctcarrl v++g++Gdal+++lve  ++++vg +
  lcl|FitnessBrowser__ANA3:7023382 234 GHPGKILALEMGGNNPLIIKGVADIKAAVHDILQSAYISSGQRCTCARRLYVEQGEQGDALVAKLVEAVKQIKVGPW 310
                                       ***************************************************************************** PP

                         TIGR03240 309 daepqpflGavisekaakellaaqekllalggksllelkqleeeaalltpgiidvtevaevpdeeyfgpllkvlryk 385
                                       +a+pqpf+G++ise aak ++aaq++l++lgg sl+el++l+++++l++pg+idvt+v e+pdeeyfgpll+++ry+
  lcl|FitnessBrowser__ANA3:7023382 311 NAQPQPFMGSMISEAAAKGMVAAQANLQNLGGVSLVELSHLQAGTGLVSPGLIDVTAVGELPDEEYFGPLLQLVRYS 387
                                       ***************************************************************************** PP

                         TIGR03240 386 dfdealaeanntrfGlaaGllsddrelydkflleiraGivnwnkpltGassaapfGGiGasGnhrpsayyaadycay 462
                                       dfd+a++ an+tr+Gl+aG+l+d+r+ y++fl +iraGivnwnk++tGas+aapfGG+GasGnhr+sa+yaadycay
  lcl|FitnessBrowser__ANA3:7023382 388 DFDQAIKLANQTRYGLSAGILADSRDDYEYFLARIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAY 464
                                       ***************************************************************************** PP

                         TIGR03240 463 pvasleadslalpatlspGlk 483
                                       pvas+ead ++lpa+lspGl+
  lcl|FitnessBrowser__ANA3:7023382 465 PVASVEADAVSLPASLSPGLS 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 30.51
//
[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:

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:

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:

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:

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