GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Shewanella halifaxensis HAW-EB4

Align 4-aminobutyrate aminotransferase; EC 2.6.1.19 (characterized, see rationale)
to candidate WP_012276125.1 SHAL_RS05105 4-aminobutyrate--2-oxoglutarate transaminase

Query= uniprot:A1S8Y2
         (425 letters)



>NCBI__GCF_000019185.1:WP_012276125.1
          Length = 425

 Score =  706 bits (1822), Expect = 0.0
 Identities = 347/420 (82%), Positives = 390/420 (92%)

Query: 4   TNDSLMVRRRAAVAGGVGQIHPVFTERAENATVWDVEGREYIDFAGGIAVLNTGHLHPKV 63
           TN+SLMVRR+AAVA GVGQIHP++T+RAENATVWDVEGRE+IDFAGGIAVLNTGHLH KV
Sbjct: 3   TNESLMVRRQAAVANGVGQIHPIYTQRAENATVWDVEGREFIDFAGGIAVLNTGHLHDKV 62

Query: 64  KAAVAEQLEKFSHTCFMVLGYESYVAVCEKLNQLVPGDFAKKSALFTSGSEAVENAIKVA 123
           KAAVAEQLE FSHTCFMVLGYE+Y+ VCEKLN LVPGDFAKK+ALFTSGSEAVENA+KVA
Sbjct: 63  KAAVAEQLELFSHTCFMVLGYENYIQVCEKLNHLVPGDFAKKTALFTSGSEAVENAVKVA 122

Query: 124 RAYTKRAGVIAFTSGYHGRTMAALALTGKVAPYSKGMGLMQANVFRAEFPCALHGVSEDD 183
           RAYTKR+GVIAFTSGYHGRTMAALALTGKVAPYSKGMGLM ANVFRAEFPCALHGV++DD
Sbjct: 123 RAYTKRSGVIAFTSGYHGRTMAALALTGKVAPYSKGMGLMSANVFRAEFPCALHGVTDDD 182

Query: 184 AMASIERIFKNDAEPSDIAAIILEPVQGEGGFYAATPGFMKRLRELCDREGIMLIADEVQ 243
           A+ASIERIFKNDAEP DIAAII+EPVQGEGGFY  +  FM+RLR+LC + GIMLIADEVQ
Sbjct: 183 AIASIERIFKNDAEPDDIAAIIIEPVQGEGGFYHTSVEFMQRLRQLCHKHGIMLIADEVQ 242

Query: 244 TGAGRTGTFFAMEQMGVAADITTFAKSIAGGFPLSGITGRAEVMDAIGPGGLGGTYGGSP 303
           TGAGRTGTFFAMEQMGV+ADITTFAKSIAGGFPLSGITGRAEVMD+IG GGLGGTYGGSP
Sbjct: 243 TGAGRTGTFFAMEQMGVSADITTFAKSIAGGFPLSGITGRAEVMDSIGAGGLGGTYGGSP 302

Query: 304 LACAAALAVIEVFEEEKLLERSNAIGQTIKSAIGELASRYPQIAEVRGLGSMIAIELMEN 363
           LACAAALAVIEVFEEE+LL+R+NA+G  +K ++  +A+++ QI +VRGLG+MIA+ELM+ 
Sbjct: 303 LACAAALAVIEVFEEEQLLQRANALGAKLKESLKAMAAKHEQIFDVRGLGAMIAVELMQE 362

Query: 364 GKPAPEYCPQVLTEARNRGLILLSCGTYGNVLRILVPITAPDEQIQRGLEIMAECFEAVL 423
           GKPAPE C Q+L EAR++GLILLSCGTYGNVLRILVP+TAPDE + RGLEI+  CF+ VL
Sbjct: 363 GKPAPELCAQMLKEARDKGLILLSCGTYGNVLRILVPLTAPDELVDRGLEIIRACFDVVL 422


Lambda     K      H
   0.319    0.136    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: 644
Number of extensions: 11
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: 425
Length of database: 425
Length adjustment: 32
Effective length of query: 393
Effective length of database: 393
Effective search space:   154449
Effective search space used:   154449
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_012276125.1 SHAL_RS05105 (4-aminobutyrate--2-oxoglutarate transaminase)
to HMM TIGR00700 (gabT: 4-aminobutyrate transaminase (EC 2.6.1.19))

# 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/TIGR00700.hmm
# target sequence database:        /tmp/gapView.2470452.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00700  [M=420]
Accession:   TIGR00700
Description: GABAtrnsam: 4-aminobutyrate transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-159  517.0   4.6   1.9e-159  516.7   4.6    1.0  1  NCBI__GCF_000019185.1:WP_012276125.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000019185.1:WP_012276125.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  516.7   4.6  1.9e-159  1.9e-159       2     417 ..      10     417 ..       9     419 .. 0.98

  Alignments for each domain:
  == domain 1  score: 516.7 bits;  conditional E-value: 1.9e-159
                             TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvp 74 
                                           rr+aav++Gvg   ++++++ae+a++ dv+G+++id+a+giavln+Gh h kv +av +q+e + ht+f+v+ 
  NCBI__GCF_000019185.1:WP_012276125.1  10 RRQAAVANGVGQIHPIYTQRAENATVWDVEGREFIDFAGGIAVLNTGHLHDKVKAAVAEQLELFSHTCFMVLG 82 
                                           89*********************************************************************** PP

                             TIGR00700  75 yesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPy 147
                                           ye y+++ ekln + Pg   kk++l++sG+eavenavk+ar+yt+r gv+af+ g+hGrt  ++alt+kv+Py
  NCBI__GCF_000019185.1:WP_012276125.1  83 YENYIQVCEKLNHLVPGDFAKKTALFTSGSEAVENAVKVARAYTKRSGVIAFTSGYHGRTMAALALTGKVAPY 155
                                           ************************************************************************* PP

                             TIGR00700 148 kiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelv 220
                                             G+G ++++v+ra +p  +++ +       dd +a+ie++f+ d e++++aa+++ePvqGeGGf  ++ e++
  NCBI__GCF_000019185.1:WP_012276125.1 156 SKGMGLMSANVFRAEFPCALHGVTD------DDAIASIERIFKNDAEPDDIAAIIIEPVQGEGGFYHTSVEFM 222
                                           *********************9877......77899************************************* PP

                             TIGR00700 221 aavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglG 293
                                           + +++lc++hgi+liadevqtG  rtG++fa+e +++  d+ t aks+a+G+Plsg++Grae++d+  +GglG
  NCBI__GCF_000019185.1:WP_012276125.1 223 QRLRQLCHKHGIMLIADEVQTGAGRTGTFFAMEQMGVSADITTFAKSIAGGFPLSGITGRAEVMDSIGAGGLG 295
                                           ************************************************************************* PP

                             TIGR00700 294 GtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelvdpdttePd 366
                                           Gty+G+Pla+aaalav+++ eee l +ra+ +g  +k+ l  + ++ ++i dvrglGamiavel++ +  +P 
  NCBI__GCF_000019185.1:WP_012276125.1 296 GTYGGSPLACAAALAVIEVFEEEQLLQRANALGAKLKESLKAMAAKHEQIFDVRGLGAMIAVELMQEG--KPA 366
                                           ****************************************************************9765..566 PP

                             TIGR00700 367 aalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaa 417
                                             l++++ ++a+ +Gl+ll++G +Gn++r+l Plt +del+d gl+i++a 
  NCBI__GCF_000019185.1:WP_012276125.1 367 PELCAQMLKEARDKGLILLSCGTYGNVLRILVPLTAPDELVDRGLEIIRAC 417
                                           678899999**************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (425 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: 00:00:00.01
# Mc/sec: 14.87
//
[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:

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