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 WP_086510803.1 BZY95_RS15480 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_002151265.1:WP_086510803.1 Length = 430 Score = 429 bits (1103), Expect = e-125 Identities = 211/421 (50%), Positives = 281/421 (66%) Query: 3 SNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKV 62 +N +L + + + + G FADRAEN +WD +G +DFAGGI VLN GH HPKV Sbjct: 2 NNAQLNELKQRYVANGAASPATQFADRAENALIWDADGNRIIDFAGGIGVLNIGHRHPKV 61 Query: 63 VAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIA 122 V AV+AQL K+ HTC V+ YE Y+++ E ++Q P K +L +G+EA+ENAVKIA Sbjct: 62 VEAVKAQLDKVMHTCQTVMPYEGYVKVAEKLSQVTPVRGHAKVMLANSGAEALENAVKIA 121 Query: 123 RAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDD 182 RAAT ++ I F G YHGRT T+A+ GKV PY++ G MPG+V+RA YP P HG+SED+ Sbjct: 122 RAATGKNNVICFDGGYHGRTFMTMAMNGKVAPYASDFGTMPGNVFRAPYPVPYHGVSEDE 181 Query: 183 AIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQ 242 AI + K DA P D AAIV+EPV GEGGFY + +F++ +R +CDEHG+++I DEVQ Sbjct: 182 AIRGLKMAIKTDANPRDTAAIVLEPVLGEGGFYPAPASFLKAIREICDEHGMLMIVDEVQ 241 Query: 243 SGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNP 302 SG GRTG LFA+E GV PD+ T AKS+A G P++ V G +VMDA P LGGTY GNP Sbjct: 242 SGFGRTGKLFAIEHSGVEPDIITMAKSMADGMPISAVVGTDKVMDASGPNSLGGTYTGNP 301 Query: 303 IACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFED 362 ++C A L VL VFE+EN+L+K+ LG KL + + R +GAM A++L D Sbjct: 302 LSCAATLAVLDVFEEENILEKSMALGDKLAKRFAQWQRDFDCVDNARNMGAMAALDLVTD 361 Query: 363 GDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQCFD 422 + PDA L A + +AR+KGLILLSCG Y N +R L+P+TIED + +GL+I+ Sbjct: 362 KAKHTPDADLAAALCKKAREKGLILLSCGLYGNTIRFLMPVTIEDEILEEGLDIVEAALT 421 Query: 423 E 423 E 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: 510 Number of extensions: 16 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: 430 Length adjustment: 32 Effective length of query: 394 Effective length of database: 398 Effective search space: 156812 Effective search space used: 156812 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_086510803.1 BZY95_RS15480 (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.4024.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-163 529.2 2.0 3.4e-163 529.0 2.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086510803.1 BZY95_RS15480 4-aminobutyrate--2 Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086510803.1 BZY95_RS15480 4-aminobutyrate--2-oxoglutarate transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 529.0 2.0 3.4e-163 3.4e-163 4 419 .. 11 421 .. 8 422 .. 0.98 Alignments for each domain: == domain 1 score: 529.0 bits; conditional E-value: 3.4e-163 TIGR00700 4 aaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqv 72 + +v++G + ++ +a +ae+a + d dGnr+id+a+gi+vln+Gh+hPkvveavk q+++++ht+ +v lcl|NCBI__GCF_002151265.1:WP_086510803.1 11 QRYVANGAASPATQFADRAENALIWDADGNRIIDFAGGIGVLNIGHRHPKVVEAVKAQLDKVMHTCQTV 79 56799999999********************************************************** PP TIGR00700 73 vpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmalt 141 +pye+yv++aekl++++P+ g++k +l nsGaea+enavkiar+ tg++ v++f++g+hGrt++tma+ lcl|NCBI__GCF_002151265.1:WP_086510803.1 80 MPYEGYVKVAEKLSQVTPVRGHAKVMLANSGAEALENAVKIARAATGKNNVICFDGGYHGRTFMTMAMN 148 ********************************************************************* PP TIGR00700 142 akvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeG 210 +kv+Py + fG ++++v+raP+p +y++ + d+ ++ ++ ++d ++++ aa+vlePv GeG lcl|NCBI__GCF_002151265.1:WP_086510803.1 149 GKVAPYASDFGTMPGNVFRAPYPVPYHGVSE------DEAIRGLKMAIKTDANPRDTAAIVLEPVLGEG 211 ***************************9988......4556678888899******************* PP TIGR00700 211 GfivpakelvaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvG 279 Gf ++ +++a++++c+ehg+++i devq+Gf rtGklfaieh +++Pd+it+aks+adG+P+s+vvG lcl|NCBI__GCF_002151265.1:WP_086510803.1 212 GFYPAPASFLKAIREICDEHGMLMIVDEVQSGFGRTGKLFAIEHSGVEPDIITMAKSMADGMPISAVVG 280 ********************************************************************* PP TIGR00700 280 raeildapapGglGGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrg 348 +++da+ p lGGty+GnPl++aa+lavld+ eee + e++ +g + ++ ++++ ++ + + r+ lcl|NCBI__GCF_002151265.1:WP_086510803.1 281 TDKVMDASGPNSLGGTYTGNPLSCAATLAVLDVFEEENILEKSMALGDKLAKRFAQWQRDFDCVDNARN 349 ********************************************************************* PP TIGR00700 349 lGamiavelv.dpdttePdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkilea 416 +Gam+a++lv d + Pda la+++ ++a+++Gl+ll++G++Gn ir+l+P+ti de+l+egl+i+ea lcl|NCBI__GCF_002151265.1:WP_086510803.1 350 MGAMAALDLVtDKAKHTPDADLAAALCKKAREKGLILLSCGLYGNTIRFLMPVTIEDEILEEGLDIVEA 418 **********8888999**************************************************** PP TIGR00700 417 ala 419 al+ lcl|NCBI__GCF_002151265.1:WP_086510803.1 419 ALT 421 996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (430 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: 00:00:00.02 # Mc/sec: 8.15 // [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