Alignments for a candidate for astD in Marinobacter guineae M3B

GapMind for catabolism of small carbon sources

Alignments for a candidate for astD in Marinobacter guineae M3B

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate WP_099617512.1 CLH62_RS07755 succinylglutamate-semialdehyde dehydrogenase

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



>NCBI__GCF_002744735.1:WP_099617512.1
          Length = 491

 Score =  624 bits (1610), Expect = 0.0
 Identities = 311/481 (64%), Positives = 372/481 (77%), Gaps = 1/481 (0%)

Query: 4   FINGQWLAGEGKEMQSKNPANGEVIWQGKAAVPAQVQAAVMAARDAQFEWFMLGFEGRQA 63
           FI+G WL G G   +S  P  GE +W G++A    V AAV  AR+A  +W    F  RQA
Sbjct: 9   FIDGLWLQGHGIPFESVQPVTGETVWDGESANLEDVDAAVREARNAFLKWQRKSFAERQA 68

Query: 64  IVEAYRNELEANKAELAEVIAQETGKPRWETATEAAAMIGKIGLSVSAYHKRTGTEVNEG 123
           +VEA+   LEANK +LA  I  ETGKP WE+ TE AAMIGKIG+SV AY+ RTG   ++ 
Sbjct: 69  VVEAFGELLEANKEDLAHQIGLETGKPLWESRTEVAAMIGKIGISVKAYNDRTGHSESDV 128

Query: 124 AAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKVAELMLKL 183
           A G AVLRH+PHGVVAVFGPYNFPGHLPNGHIVPA+LAGNTVVFKPSELTP VAE+++KL
Sbjct: 129 AGGHAVLRHRPHGVVAVFGPYNFPGHLPNGHIVPAVLAGNTVVFKPSELTPGVAEVIVKL 188

Query: 184 WEKAGLPAGVINLVQGEVETGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKILALE 243
           WEKAG+P GVINLVQG  +TGK+LASHP +DGLFFTGSS  GHLLH+Q+ G P KILALE
Sbjct: 189 WEKAGIPDGVINLVQGGADTGKSLASHPMIDGLFFTGSSTVGHLLHKQFGGQPEKILALE 248

Query: 244 MGGNNPLIVKGVSDTRAAIHDIIQSAFISSGQRCTCARRLYVEKGAEGDKLLAGLVEAVK 303
           MGGNNPLIV+ V D   A+H  +QSAF+S+GQRCTCARRL V KG +GD  L  LV+   
Sbjct: 249 MGGNNPLIVQDVHDLDGAVHHALQSAFLSAGQRCTCARRLLVPKGKKGDAFLDRLVQVAS 308

Query: 304 AIKVGPWNADPQPFMGSMISETAAKGMLDAQRNLLNLGAKSLVEMTHLQAGTGLVSPGLI 363
            IKVG ++ADPQPFMGS+IS  AA  +L AQ ++L  G KSL+EM  L+  TGL+SPG++
Sbjct: 309 RIKVGEFDADPQPFMGSVISAEAADKLLAAQASMLEKGGKSLLEMKSLKPDTGLLSPGIV 368

Query: 364 DVTEVIELPDEEYFGPLLQVVRYTSFDEAIRLANDTRYGLSAGILADDKADYEYFLARIR 423
           DVT  +EL DEE+FGPLL V RY SFD+A+ LANDTRYGLSAGIL+DD+  Y+  +  +R
Sbjct: 369 DVTG-LELTDEEFFGPLLTVHRYKSFDDALELANDTRYGLSAGILSDDRKLYDRLVEEVR 427

Query: 424 AGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASMEADSVTLPASLSPG 483
           AGIVNWN+ +TGAS AAPFGGVGASGNHR SA+YAADYCA+P+AS+EA    LP +L+PG
Sbjct: 428 AGIVNWNRPLTGASSAAPFGGVGASGNHRPSAYYAADYCAWPMASLEAGKSELPDTLAPG 487

Query: 484 L 484
           L
Sbjct: 488 L 488


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: 786
Number of extensions: 22
Number of successful extensions: 2
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: 491
Length adjustment: 34
Effective length of query: 452
Effective length of database: 457
Effective search space:   206564
Effective search space used:   206564
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 WP_099617512.1 CLH62_RS07755 (succinylglutamate-semialdehyde dehydrogenase)
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.2857404.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.3e-251  819.3   0.0     6e-251  819.2   0.0    1.0  1  NCBI__GCF_002744735.1:WP_099617512.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002744735.1:WP_099617512.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  819.2   0.0    6e-251    6e-251       1     484 []       8     490 ..       8     490 .. 1.00

  Alignments for each domain:
  == domain 1  score: 819.2 bits;  conditional E-value: 6e-251
                             TIGR03240   1 lfidGkwraGqGeslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaelleee 73 
                                           lfidG w +G+G  +es++pvt+e++w+g++a+ ++v++av+ ar+af +w r s++er+avv+ f elle +
  NCBI__GCF_002744735.1:WP_099617512.1   8 LFIDGLWLQGHGIPFESVQPVTGETVWDGESANLEDVDAAVREARNAFLKWQRKSFAERQAVVEAFGELLEAN 80 
                                           59*********************************************************************** PP

                             TIGR03240  74 keelaeviaketgkplweartevasmvakvaisikayeertGekeseladakavlrhrphGvlavfGpynfpG 146
                                           ke+la+ i+ etgkplwe+rteva+m++k+ is+kay++rtG++es++a ++avlrhrphGv+avfGpynfpG
  NCBI__GCF_002744735.1:WP_099617512.1  81 KEDLAHQIGLETGKPLWESRTEVAAMIGKIGISVKAYNDRTGHSESDVAGGHAVLRHRPHGVVAVFGPYNFPG 153
                                           ************************************************************************* PP

                             TIGR03240 147 hlpnGhivpallaGntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeedidGllftGs 219
                                           hlpnGhivpa+laGntvvfkpseltp vae +vklwekaG+p+Gv+nlvqG+ +tGk+la+++ idGl+ftGs
  NCBI__GCF_002744735.1:WP_099617512.1 154 HLPNGHIVPAVLAGNTVVFKPSELTPGVAEVIVKLWEKAGIPDGVINLVQGGADTGKSLASHPMIDGLFFTGS 226
                                           ************************************************************************* PP

                             TIGR03240 220 sntGallhrqlagrpekilalelGGnnplvveevkdidaavhlivqsafisaGqrctcarrllvkdgaeGdal 292
                                           s+ G+llh+q++g+pekilale+GGnnpl+v++v+d+d+avh+++qsaf+saGqrctcarrllv++g++Gda+
  NCBI__GCF_002744735.1:WP_099617512.1 227 STVGHLLHKQFGGQPEKILALEMGGNNPLIVQDVHDLDGAVHHALQSAFLSAGQRCTCARRLLVPKGKKGDAF 299
                                           ************************************************************************* PP

                             TIGR03240 293 lerlvevaerltvgkydaepqpflGavisekaakellaaqekllalggksllelkqleeeaalltpgiidvte 365
                                           l+rlv+va+r++vg++da+pqpf+G+vis++aa++llaaq+++l++ggkslle+k+l+ +++ll+pgi+dvt+
  NCBI__GCF_002744735.1:WP_099617512.1 300 LDRLVQVASRIKVGEFDADPQPFMGSVISAEAADKLLAAQASMLEKGGKSLLEMKSLKPDTGLLSPGIVDVTG 372
                                           ************************************************************************* PP

                             TIGR03240 366 vaevpdeeyfgpllkvlrykdfdealaeanntrfGlaaGllsddrelydkflleiraGivnwnkpltGassaa 438
                                           + e+ dee+fgpll+v ryk+fd+al+ an+tr+Gl+aG+lsddr+lyd++++e+raGivnwn+pltGassaa
  NCBI__GCF_002744735.1:WP_099617512.1 373 L-ELTDEEFFGPLLTVHRYKSFDDALELANDTRYGLSAGILSDDRKLYDRLVEEVRAGIVNWNRPLTGASSAA 444
                                           8.9********************************************************************** PP

                             TIGR03240 439 pfGGiGasGnhrpsayyaadycaypvasleadslalpatlspGlkl 484
                                           pfGG+GasGnhrpsayyaadyca+p+aslea + +lp tl+pGl++
  NCBI__GCF_002744735.1:WP_099617512.1 445 PFGGVGASGNHRPSAYYAADYCAWPMASLEAGKSELPDTLAPGLNF 490
                                           *******************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (484 nodes)
Target sequences:                          1  (491 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 33.68
//
[ok]

This GapMind analysis is from Sep 24 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