Align 4-aminobutyrate aminotransferase; EC 2.6.1.19; (S)-3-amino-2-methylpropionate transaminase; EC 2.6.1.22; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT (uncharacterized)
to candidate WP_076476008.1 BW971_RS02060 4-aminobutyrate--2-oxoglutarate transaminase
Query= curated2:P63505 (449 letters) >NCBI__GCF_900156495.1:WP_076476008.1 Length = 452 Score = 547 bits (1410), Expect = e-160 Identities = 283/439 (64%), Positives = 330/439 (75%), Gaps = 8/439 (1%) Query: 4 LQQSRRLVTEIPGPASQALTHRRAAAVSSGVGVTLPVFVARAGGGIVEDVDGNRLIDLGS 63 L Q R LVT +PGP S AL RRAAAV++GVG +P++ A A GGI+ DVDGN LIDLGS Sbjct: 9 LPQKRHLVTPLPGPESSALAKRRAAAVAAGVGSVVPIYAADADGGIIVDVDGNSLIDLGS 68 Query: 64 GIAVTTIGNSSPRVVDAVRTQVAEFTHTCFMVTPYEGYVAVAEQLNRITPGSGPKRSVLF 123 GIAVT +G S+P V DAV Q FTHTCFMVTPYEGYVAVAE+LN +TPG KRSVLF Sbjct: 69 GIAVTGVGASNPAVADAVAAQAHHFTHTCFMVTPYEGYVAVAEKLNELTPGDHEKRSVLF 128 Query: 124 NSGAEAVENAVKIARSYTGKPAVVAFDHAYHGRTNLTMALTAKSMPYKSGFGPFAPEIYR 183 NSGAEAVENAVK+AR TG+ A+VAFDHAYHGRTNLTMALTAK+ PYK FGPFAPEIYR Sbjct: 129 NSGAEAVENAVKVARLATGRDAIVAFDHAYHGRTNLTMALTAKTQPYKYNFGPFAPEIYR 188 Query: 184 APLSYPYRDGLLDKQLATNGELAAARAIGVIDKQVGANNLAALVIEPIQGEGGFIVPAEG 243 P+SYPYRD L T+G AA RAI I+ Q+G +A L+IEPIQGEGGFIVPA G Sbjct: 189 MPMSYPYRD-----DLGTDGVSAAKRAIRQIETQIGGEAVAGLLIEPIQGEGGFIVPAPG 243 Query: 244 FLPALLDWCRKNHVVFIADEVQTGFARTGAMFACEHEGPDGLEPDLICTAKGIADGLPLS 303 FL L +W R N VVFIADEVQ GF RTG FA E E G+ PD++ TAKGIA G+PLS Sbjct: 244 FLTTLAEWARDNGVVFIADEVQAGFCRTGTWFASEAE---GIVPDIVTTAKGIAGGMPLS 300 Query: 304 AVTGRAEIMNAPHVGGLGGTFGGNPVACAAALATIATIESDGLIERARQIERLVTDRLTT 363 A+TGRA++++ H GGLGGT+GGNPVACAAALATIA +E L RA IE + RL T Sbjct: 301 AITGRADLLDKVHPGGLGGTYGGNPVACAAALATIAEMEELDLNARAHHIEEIALPRLRT 360 Query: 364 LQAVDDRIGDVRGRGAMIAVELVKSGTTEPDAGLTERLATAAHAAGVIILTCGMFGNIIR 423 L D IGDVRGRGAM+A+E+V+ GT P L +++A AA AGV+IL G FGN+IR Sbjct: 361 LADDLDVIGDVRGRGAMLAIEIVEPGTDTPAPALAKKVAAAALEAGVVILVTGTFGNVIR 420 Query: 424 LLPPLTIGDELLSEGLDIV 442 LLPPL I DE L +G+D++ Sbjct: 421 LLPPLVIDDETLVDGIDVL 439 Lambda K H 0.319 0.137 0.397 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: 680 Number of extensions: 28 Number of successful extensions: 3 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: 449 Length of database: 452 Length adjustment: 33 Effective length of query: 416 Effective length of database: 419 Effective search space: 174304 Effective search space used: 174304 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_076476008.1 BW971_RS02060 (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.3549537.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-176 572.2 6.3 3.1e-176 572.0 6.3 1.0 1 NCBI__GCF_900156495.1:WP_076476008.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900156495.1:WP_076476008.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 572.0 6.3 3.1e-176 3.1e-176 1 419 [. 29 444 .. 29 445 .. 0.97 Alignments for each domain: == domain 1 score: 572.0 bits; conditional E-value: 3.1e-176 TIGR00700 1 qrraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvv 73 +rraaav+ Gvg +++++aa a+g+++ dvdGn lidl++giav+ vG s+P v +av q++++tht+f+v+ NCBI__GCF_900156495.1:WP_076476008.1 29 KRRAAAVAAGVGSVVPIYAADADGGIIVDVDGNSLIDLGSGIAVTGVGASNPAVADAVAAQAHHFTHTCFMVT 101 69*********************************************************************** PP TIGR00700 74 pyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkP 146 pye+yv++aekln+++Pg +ek++vl+nsGaeavenavk+ar tgr+++vaf++++hGrtnltmaltak++P NCBI__GCF_900156495.1:WP_076476008.1 102 PYEGYVAVAEKLNELTPGDHEKRSVLFNSGAEAVENAVKVARLATGRDAIVAFDHAYHGRTNLTMALTAKTQP 174 ************************************************************************* PP TIGR00700 147 ykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvad..veaeqvaavvlePvqGeGGfivpak 217 yk+ fGPfape+yr+P++y+yrd ++ +d++ aa +a+ ++ ++ e va +++eP+qGeGGfivpa NCBI__GCF_900156495.1:WP_076476008.1 175 YKYNFGPFAPEIYRMPMSYPYRDDLG-----TDGVSAAKRAIRQIEtqIGGEAVAGLLIEPIQGEGGFIVPAP 242 ***********************999.....55555555555555444************************* PP TIGR00700 218 elvaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapG 290 ++++++a++ +++g+v+iadevq+Gf rtG+ fa e e+ +Pd++t+ak++a+G+Pls+++Gra++ld +pG NCBI__GCF_900156495.1:WP_076476008.1 243 GFLTTLAEWARDNGVVFIADEVQAGFCRTGTWFASEAEGIVPDIVTTAKGIAGGMPLSAITGRADLLDKVHPG 315 ************************************************************************* PP TIGR00700 291 glGGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelvdpdtt 363 glGGty+GnP+a+aaala+++ +ee l+ ra++i+++ +l +l + ++igdvrg+Gam+a+e+v+p+t NCBI__GCF_900156495.1:WP_076476008.1 316 GLGGTYGGNPVACAAALATIAEMEELDLNARAHHIEEIALPRLRTLADDLDVIGDVRGRGAMLAIEIVEPGTD 388 ************************************************************************* PP TIGR00700 364 ePdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaala 419 P ala+k+aaaal+aG+++l +G fGn+irll+Pl+i de l +g+++le++l NCBI__GCF_900156495.1:WP_076476008.1 389 TPAPALAKKVAAAALEAGVVILVTGTFGNVIRLLPPLVIDDETLVDGIDVLEQSLH 444 ****************************************************9885 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (452 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: 14.45 // [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