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.
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:
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