Align Probable 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_207545101.1 BM299_RS02525 4-aminobutyrate--2-oxoglutarate transaminase
Query= curated2:P94427 (436 letters) >NCBI__GCF_900115975.1:WP_207545101.1 Length = 434 Score = 443 bits (1139), Expect = e-129 Identities = 209/423 (49%), Positives = 298/423 (70%) Query: 9 TTAQWQQKRDQFVSKGVSNGNRSLAVKGEGAELYDLDGRRFIDFAGAIGTLNVGHSHPKV 68 T A+ ++ Q +++G+SN K +GA + D++G+ +IDF G IGTLN GH V Sbjct: 4 TNAELVARKHQLIARGISNSTEVFVEKAQGATIVDVEGKEYIDFYGGIGTLNAGHCPAPV 63 Query: 69 VEAVKRQAEELIHPGFNVMMYPTYIELAEKLCGIAPGSHEKKAIFLNSGAEAVENAVKIA 128 VEA+K QAE+L+H F V MY Y++LAEKL + PG+ +K+ +F+NSGAE VENAVKIA Sbjct: 64 VEAIKNQAEKLLHTCFMVTMYEPYLDLAEKLIELTPGNFDKRVMFVNSGAECVENAVKIA 123 Query: 129 RKYTKRQGVVSFTRGFHGRTNMTMSMTSKVKPYKFGFGPFAPEVYQAPFPYYYQKPAGMS 188 R Y KR G++SF FHGRT MTMS+TSKVKPYKFGFGPFAPEVY+ P Y Y+ + Sbjct: 124 RSYAKRTGIISFECAFHGRTLMTMSLTSKVKPYKFGFGPFAPEVYKIPSAYCYRCTYRST 183 Query: 189 DESYDDMVIQAFNDFFIASVAPETVACVVMEPVQGEGGFIIPSKRFVQHVASFCKEHGIV 248 ++ F+ F A V PE +A +++EPVQGEGGFI+P F+ + C +HGI+ Sbjct: 184 YPECGLHCLEQFDRMFAAEVPPENIAAMIIEPVQGEGGFIVPPPEFLPGLRKICDKHGII 243 Query: 249 FVADEIQTGFARTGTYFAIEHFDVVPDLITVSKSLAAGLPLSGVIGRAEMLDAAAPGELG 308 +ADE+QTGF RTG FA EHF + PDL+T++KS+AAG+PLS V+G+A++++A PGE+G Sbjct: 244 LIADEVQTGFGRTGKMFACEHFGLEPDLMTMAKSIAAGMPLSAVVGKADIMNAPNPGEIG 303 Query: 309 GTYAGSPLGCAAALAVLDIIEEEGLNERSEEIGKIIEDKAYEWKQEFPFIGDIRRLGAMA 368 GTY+G+P+ CAA LA +D ++++ L ER+ IG + + ++++P IGD+R LGAM Sbjct: 304 GTYSGNPVSCAAGLATIDFMQQQNLVERANVIGDKTKQRMLAMQEKYPIIGDVRGLGAMN 363 Query: 369 AIEIVKDPDTREPDKTKAAAIAAYANQNGLLLLTAGINGNIIRFLTPLVISDSLLNEGLS 428 A+E+VKD +T+EP K + AA+ + NG++++ AGI N++R L PLVI+D L +GL Sbjct: 364 AMELVKDRNTKEPAKEETAAVIKHCVDNGVIVIGAGIFSNVVRTLIPLVITDEQLEKGLD 423 Query: 429 ILE 431 +LE Sbjct: 424 VLE 426 Lambda K H 0.319 0.136 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: 471 Number of extensions: 9 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: 436 Length of database: 434 Length adjustment: 32 Effective length of query: 404 Effective length of database: 402 Effective search space: 162408 Effective search space used: 162408 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 (21.7 bits) S2: 51 (24.3 bits)
Align candidate WP_207545101.1 BM299_RS02525 (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.1821650.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-179 581.1 0.7 6.3e-179 580.9 0.7 1.0 1 NCBI__GCF_900115975.1:WP_207545101.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900115975.1:WP_207545101.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 580.9 0.7 6.3e-179 6.3e-179 2 419 .. 11 430 .. 10 431 .. 0.97 Alignments for each domain: == domain 1 score: 580.9 bits; conditional E-value: 6.3e-179 TIGR00700 2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvp 74 r+++ +++G++++++v++ ka+ga++ dv+G+++id+ +gi++ln Gh vvea+k+q+e+l ht+f+v++ NCBI__GCF_900115975.1:WP_207545101.1 11 RKHQLIARGISNSTEVFVEKAQGATIVDVEGKEYIDFYGGIGTLNAGHCPAPVVEAIKNQAEKLLHTCFMVTM 83 78899******************************************************************** PP TIGR00700 75 yesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPy 147 ye y++laekl +++Pg +k+ +++nsGae venavkiar+y++r g+++f+ +fhGrt +tm+lt+kvkPy NCBI__GCF_900115975.1:WP_207545101.1 84 YEPYLDLAEKLIELTPGNFDKRVMFVNSGAECVENAVKIARSYAKRTGIISFECAFHGRTLMTMSLTSKVKPY 156 ************************************************************************* PP TIGR00700 148 kiGfGPfapevyraPlpydyrdialdk.qeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakel 219 k+GfGPfapevy++P +y yr + + e+ l+ ++++f a+v +e++aa+++ePvqGeGGfivp+ e+ NCBI__GCF_900115975.1:WP_207545101.1 157 KFGFGPFAPEVYKIPSAYCYRCTYRSTyPECGLHCLEQFDRMFAAEVPPENIAAMIIEPVQGEGGFIVPPPEF 229 *******************99876544133334499************************************* PP TIGR00700 220 vaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGgl 292 ++ ++++c++hgi+liadevqtGf rtGk+fa+eh++ +Pdl+t+aks+a+G+Pls+vvG+a+i++ap+pG++ NCBI__GCF_900115975.1:WP_207545101.1 230 LPGLRKICDKHGIILIADEVQTGFGRTGKMFACEHFGLEPDLMTMAKSIAAGMPLSAVVGKADIMNAPNPGEI 302 ************************************************************************* PP TIGR00700 293 GGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelv.dpdtte 364 GGty+GnP+++aa la++d ++++ l+era+ ig k++++ ++e+ p igdvrglGam a+elv d +t+e NCBI__GCF_900115975.1:WP_207545101.1 303 GGTYSGNPVSCAAGLATIDFMQQQNLVERANVIGDKTKQRMLAMQEKYPIIGDVRGLGAMNAMELVkDRNTKE 375 ******************************************************************999**** PP TIGR00700 365 PdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaala 419 P + ++++ ++ +G++++ aGif n++r l Pl+i+de+l++gl++le+a+a NCBI__GCF_900115975.1:WP_207545101.1 376 PAKEETAAVIKHCVDNGVIVIGAGIFSNVVRTLIPLVITDEQLEKGLDVLEQAVA 430 **************************************************99875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (434 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: 17.72 // [ok]
This GapMind analysis is from Apr 09 2024. 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