Align 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized)
to candidate 5210744 Shew_3172 4-aminobutyrate aminotransferase (RefSeq)
Query= SwissProt::P22256 (426 letters) >FitnessBrowser__PV4:5210744 Length = 426 Score = 463 bits (1191), Expect = e-135 Identities = 230/421 (54%), Positives = 294/421 (69%), Gaps = 1/421 (0%) Query: 3 SNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKV 62 SN EL R+ QAI RG G +P++ +RA N +WDVEG+ Y+DF GIAV NTGH HPKV Sbjct: 2 SNAELQARKVQAIARGQGNAYPVYVERALNAELWDVEGKRYIDFGTGIAVCNTGHSHPKV 61 Query: 63 VAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIA 122 VAAV+AQL SHTC V YE + L E +N+ PG KK + VTTG+EAVEN VKIA Sbjct: 62 VAAVKAQLDNFSHTCVMVNPYESAVALAEQLNRIAPGGSDKKAIFVTTGAEAVENCVKIA 121 Query: 123 RAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDD 182 RA T R G IAF+G +HGRT+ T+ALTGK+ PY G G ++ A YP HG+S D Sbjct: 122 RAHTGRRGVIAFNGGFHGRTNLTMALTGKITPYKHQFGPFAGDIFHAPYPVAFHGVSVKD 181 Query: 183 AIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQ 242 ++ +I +FK D AP D+AAIV+EPVQGEGGFYA+ P F+Q LRALCD+HGI+L+ DE+Q Sbjct: 182 SLKAIEHLFKVDIAPCDVAAIVVEPVQGEGGFYAAPPEFLQALRALCDQHGIVLVMDEIQ 241 Query: 243 SGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNP 302 +G GRTG +F+ E GV PDL T AK IAGGFPLA V G++E+MDA PGGLGGTY G+P Sbjct: 242 TGFGRTGKMFSCEHAGVEPDLMTMAKGIAGGFPLAAVVGKSEIMDAPLPGGLGGTYGGSP 301 Query: 303 IACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPE-IGDVRGLGAMIAIELFE 361 + CVAAL VL+V ++E L+++A +G L A+ E++P+ IG+VR GAMIA+EL Sbjct: 302 VGCVAALAVLEVMQEEQLVERAVKIGDSFNQALSALKEQYPQLIGEVRNQGAMIAMELVI 361 Query: 362 DGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQCF 421 DGD +P+ LT I+A A GL+LL+CG Y NV+R L LTI D + +GL F Sbjct: 362 DGDIEQPNTALTQAIIANAAAHGLVLLACGFYGNVIRFLPALTISDEIMAEGLAKFKTLF 421 Query: 422 D 422 + Sbjct: 422 E 422 Lambda K H 0.320 0.137 0.401 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: 566 Number of extensions: 19 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: 426 Length of database: 426 Length adjustment: 32 Effective length of query: 394 Effective length of database: 394 Effective search space: 155236 Effective search space used: 155236 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 5210744 Shew_3172 (4-aminobutyrate aminotransferase (RefSeq))
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.21255.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-178 580.2 5.4 1.3e-178 579.9 5.4 1.0 1 lcl|FitnessBrowser__PV4:5210744 Shew_3172 4-aminobutyrate aminot Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5210744 Shew_3172 4-aminobutyrate aminotransferase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 579.9 5.4 1.3e-178 1.3e-178 2 413 .. 9 416 .. 8 423 .. 0.98 Alignments for each domain: == domain 1 score: 579.9 bits; conditional E-value: 1.3e-178 TIGR00700 2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvpyesyv 79 r+ +a+++G g++ +v++ +a +ael dv+G+r+id+++giav n+GhshPkvv+avk q++++ ht+ +v pyes v lcl|FitnessBrowser__PV4:5210744 9 RKVQAIARGQGNAYPVYVERALNAELWDVEGKRYIDFGTGIAVCNTGHSHPKVVAAVKAQLDNFSHTCVMVNPYESAV 86 7899************************************************************************** PP TIGR00700 80 elaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPykiGfGPfape 157 +lae+ln+iaPg +kka+++++Gaeaven vkiar++tgr+gv+af++gfhGrtnltmalt+k++Pyk fGPfa++ lcl|FitnessBrowser__PV4:5210744 87 ALAEQLNRIAPGGSDKKAIFVTTGAEAVENCVKIARAHTGRRGVIAFNGGFHGRTNLTMALTGKITPYKHQFGPFAGD 164 ****************************************************************************** PP TIGR00700 158 vyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelvaavaslckehgivli 235 +++aP+p +++ ++ +d l+aie+lf++d+++ +vaa+v+ePvqGeGGf ++ e+++a++ lc++hgivl+ lcl|FitnessBrowser__PV4:5210744 165 IFHAPYPVAFHGVSV------KDSLKAIEHLFKVDIAPCDVAAIVVEPVQGEGGFYAAPPEFLQALRALCDQHGIVLV 236 ***********9988......44667**************************************************** PP TIGR00700 236 adevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglGGtyaGnPlavaaalavldii 313 de+qtGf rtGk+f++eh +++Pdl+t+ak++a+G+Pl++vvG++ei+dap pGglGGty+G+P+++ aalavl+++ lcl|FitnessBrowser__PV4:5210744 237 MDEIQTGFGRTGKMFSCEHAGVEPDLMTMAKGIAGGFPLAAVVGKSEIMDAPLPGGLGGTYGGSPVGCVAALAVLEVM 314 ****************************************************************************** PP TIGR00700 314 eeeglieraeqigklvkdklielkeevpa.igdvrglGamiavelv.dpdttePdaalaekiaaaalaaGlllltaGi 389 +ee l+era +ig ++ l lke+ p+ ig+vr++Gamia+elv d d ++P++al+++i a+a a+Gl+ll++G lcl|FitnessBrowser__PV4:5210744 315 QEEQLVERAVKIGDSFNQALSALKEQYPQlIGEVRNQGAMIAMELViDGDIEQPNTALTQAIIANAAAHGLVLLACGF 392 *************************998549***************9******************************* PP TIGR00700 390 fGniirlltPltisdelldeglki 413 +Gn+ir+l+ ltisde++ egl lcl|FitnessBrowser__PV4:5210744 393 YGNVIRFLPALTISDEIMAEGLAK 416 *********************975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (426 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 6.95 // [ok]
This GapMind analysis is from Sep 17 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