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 6937470 Sama_1626 succinylglutamic semialdehyde dehydrogenase (RefSeq)

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



>FitnessBrowser__SB2B:6937470
          Length = 495

 Score =  658 bits (1698), Expect = 0.0
 Identities = 322/483 (66%), Positives = 385/483 (79%)

Query: 4   FIKGQWHTGKGHDVASSNPANGEIIWRGQTATAEQVNAAVDAAREAQFDWFILGFDARLK 63
           FI GQW  G G    S NPANGE+IW G  A AEQV+ AV AAR A ++W  +    RL 
Sbjct: 13  FIGGQWQPGHGKGFESINPANGEVIWCGNGANAEQVDTAVKAARSAFYNWSAMPLAERLA 72

Query: 64  IVEAYRSQLEANKAELAETIAQETGKPQWETATEVAAMIGKIGLSASAYNKRTGTETNDT 123
           I+EA+ +QL  +   +A  IA+ETGK  WE+ TEVAAM GKI +S  A+++RTGT  N  
Sbjct: 73  IIEAFGAQLGEHSEAMARLIAEETGKALWESRTEVAAMTGKIAISIRAHSERTGTVENPM 132

Query: 124 PAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVVFKPSELTPKVAELMVTL 183
           P  RA +RHKPHGVVAVFGPYNFPGHLPNGHIVPAL+AGN+V+FKPSELTPKVA+  V L
Sbjct: 133 PGARAFIRHKPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVLFKPSELTPKVAQFTVEL 192

Query: 184 WEKSGLPAGVLNLVQGEVDTGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKILALE 243
           W+K+GLPAGV+NL+QGEV+TGKALA HP +DGLFFTGSS TGHLLHQQYAG PGKILALE
Sbjct: 193 WQKAGLPAGVINLLQGEVETGKALAGHPGIDGLFFTGSSNTGHLLHQQYAGQPGKILALE 252

Query: 244 MGGNNPLIIKGVADIKAAVHDILQSAYISSGQRCTCARRLYVEQGEQGDALVAKLVEAVK 303
           MGGNNPLI+K VA++ AAVHDI+QSA+ISSGQRCTCARRL++++   GDA++AKL+EA +
Sbjct: 253 MGGNNPLIVKDVANVNAAVHDIIQSAFISSGQRCTCARRLFIKKDANGDAILAKLIEASR 312

Query: 304 QIKVGPWNAQPQPFMGSMISEAAAKGMVAAQANLLSLGGVPLVELMHLQAGTGLVSPGLI 363
           QI+V    A+ QPF G+MIS  AA  MV AQ ++ SLGG+ L+EL       G V+PG+I
Sbjct: 313 QIRVDEPFAENQPFYGAMISAKAAAAMVKAQTDIQSLGGISLLELKQPDLALGFVTPGII 372

Query: 364 DVTAVSELPDEEYFGPLLQLVRYSDFDQAIKLANQTRYGLSAGILADSREDYEYFLARIR 423
           DVT V  LPDEE+FGPLL++ RY DFD AI  AN T +GLSAG+LAD+  DY++F  RIR
Sbjct: 373 DVTHVKALPDEEHFGPLLKVYRYDDFDAAIDEANNTAFGLSAGLLADNEADYDHFFRRIR 432

Query: 424 AGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASVEADAVSLPATLSPG 483
           AGIVNWNK ITGAS AAPFGG+GASGNHRASAFYAADYCAYPV+SVEA +VSLPA+LSPG
Sbjct: 433 AGIVNWNKPITGASSAAPFGGIGASGNHRASAFYAADYCAYPVSSVEASSVSLPASLSPG 492

Query: 484 LTL 486
           L++
Sbjct: 493 LSI 495


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: 873
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: 495
Length adjustment: 34
Effective length of query: 453
Effective length of database: 461
Effective search space:   208833
Effective search space used:   208833
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 6937470 Sama_1626 (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.2179.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   5.1e-249  812.8   1.1   5.7e-249  812.6   1.1    1.0  1  lcl|FitnessBrowser__SB2B:6937470  Sama_1626 succinylglutamic semia


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937470  Sama_1626 succinylglutamic semialdehyde dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  812.6   1.1  5.7e-249  5.7e-249       1     483 [.      12     494 ..      12     495 .] 1.00

  Alignments for each domain:
  == domain 1  score: 812.6 bits;  conditional E-value: 5.7e-249
                         TIGR03240   1 lfidGkwraGqGeslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaelleeekeel 77 
                                       +fi G+w+ G+G+ +es++p+++ev+w g++a+a+qv++avkaar af++w++++l+er+a+++ f ++l e+ e++
  lcl|FitnessBrowser__SB2B:6937470  12 QFIGGQWQPGHGKGFESINPANGEVIWCGNGANAEQVDTAVKAARSAFYNWSAMPLAERLAIIEAFGAQLGEHSEAM 88 
                                       69*************************************************************************** PP

                         TIGR03240  78 aeviaketgkplweartevasmvakvaisikayeertGekeseladakavlrhrphGvlavfGpynfpGhlpnGhiv 154
                                       a++ia+etgk+lwe+rteva+m +k+aisi+a++ertG++e++++ a+a++rh+phGv+avfGpynfpGhlpnGhiv
  lcl|FitnessBrowser__SB2B:6937470  89 ARLIAEETGKALWESRTEVAAMTGKIAISIRAHSERTGTVENPMPGARAFIRHKPHGVVAVFGPYNFPGHLPNGHIV 165
                                       ***************************************************************************** PP

                         TIGR03240 155 pallaGntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeedidGllftGssntGallhrqla 231
                                       pal+aGntv+fkpseltp+va+ tv+lw+kaGlpaGv+nl+qG++etGkala +++idGl+ftGssntG+llh+q+a
  lcl|FitnessBrowser__SB2B:6937470 166 PALIAGNTVLFKPSELTPKVAQFTVELWQKAGLPAGVINLLQGEVETGKALAGHPGIDGLFFTGSSNTGHLLHQQYA 242
                                       ***************************************************************************** PP

                         TIGR03240 232 grpekilalelGGnnplvveevkdidaavhlivqsafisaGqrctcarrllvkdgaeGdallerlvevaerltvgky 308
                                       g+p kilale+GGnnpl+v++v++++aavh+i+qsafis+Gqrctcarrl++k++a+Gda+l++l+e +++++v++ 
  lcl|FitnessBrowser__SB2B:6937470 243 GQPGKILALEMGGNNPLIVKDVANVNAAVHDIIQSAFISSGQRCTCARRLFIKKDANGDAILAKLIEASRQIRVDEP 319
                                       ***************************************************************************** PP

                         TIGR03240 309 daepqpflGavisekaakellaaqekllalggksllelkqleeeaalltpgiidvtevaevpdeeyfgpllkvlryk 385
                                        ae+qpf Ga+is+kaa ++++aq++++ lgg sllelkq + + +++tpgiidvt+v+ +pdee+fgpllkv+ry+
  lcl|FitnessBrowser__SB2B:6937470 320 FAENQPFYGAMISAKAAAAMVKAQTDIQSLGGISLLELKQPDLALGFVTPGIIDVTHVKALPDEEHFGPLLKVYRYD 396
                                       ***************************************************************************** PP

                         TIGR03240 386 dfdealaeanntrfGlaaGllsddrelydkflleiraGivnwnkpltGassaapfGGiGasGnhrpsayyaadycay 462
                                       dfd+a++eannt+fGl+aGll+d+++ yd+f+++iraGivnwnkp+tGassaapfGGiGasGnhr+sa+yaadycay
  lcl|FitnessBrowser__SB2B:6937470 397 DFDAAIDEANNTAFGLSAGLLADNEADYDHFFRRIRAGIVNWNKPITGASSAAPFGGIGASGNHRASAFYAADYCAY 473
                                       ***************************************************************************** PP

                         TIGR03240 463 pvasleadslalpatlspGlk 483
                                       pv+s+ea+s++lpa+lspGl+
  lcl|FitnessBrowser__SB2B:6937470 474 PVSSVEASSVSLPASLSPGLS 494
                                       *******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (484 nodes)
Target sequences:                          1  (495 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.32
//
[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