Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate Ac3H11_4179 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Query= metacyc::MONOMER-11537 (425 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4179 Length = 459 Score = 555 bits (1430), Expect = e-162 Identities = 276/417 (66%), Positives = 332/417 (79%) Query: 4 TNASLMKRREAAVPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKI 63 TNA+L+ RR AAV RGVGQ H +F A+NA + DVEGR FIDFAGGIAVLNTGH+H + Sbjct: 33 TNAALLTRRHAAVARGVGQAHDLFIQKARNAELWDVEGRRFIDFAGGIAVLNTGHLHAGV 92 Query: 64 IAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIA 123 IAAV QL+ THTCFQV+AYEPYVE+CE++N PG FAKK+LL+TTG+EAVENA+KIA Sbjct: 93 IAAVKAQLDLYTHTCFQVVAYEPYVEVCERLNTLAPGAFAKKSLLLTTGAEAVENAIKIA 152 Query: 124 RAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDD 183 RA T R GVIAFTG YHGRT +TLGLTGKV PY G G PG + AL+PN LHGVS++ Sbjct: 153 RAYTKRPGVIAFTGGYHGRTNLTLGLTGKVAPYKIGFGPFPGETYHALFPNALHGVSVEQ 212 Query: 184 SIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQ 243 ++ S+E IFKND EP +AA I+EPVQGEGGFYVAP EF+ L+ L D++GILLIADEVQ Sbjct: 213 ALHSVELIFKNDIEPERVAAFIVEPVQGEGGFYVAPPEFISGLKTLADRYGILLIADEVQ 272 Query: 244 TGAGRTGTFFAMEQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSP 303 TGAGRTGT+FA EQ V DL T AKS+AGGFPLAGV G+A+ MDA APGGLGGTYAGSP Sbjct: 273 TGAGRTGTWFASEQWPVAPDLITTAKSLAGGFPLAGVVGRADVMDAPAPGGLGGTYAGSP 332 Query: 304 IACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFEN 363 +ACAA+LAV+E F +E LL R + +G LV LK + A+ P IG+VR LGAM+A+ELFEN Sbjct: 333 VACAASLAVIEAFAQEKLLARSQDMGALLVRSLKDLAARIPAIGDVRGLGAMVAIELFEN 392 Query: 364 GDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEE 420 GD +P+AA QVVA+A +GLILLSCGT+GNV+R+LVPLT+ D L +GLAI+ + Sbjct: 393 GDLSRPDAALTKQVVAEAARRGLILLSCGTHGNVIRILVPLTASDELLHEGLAILAD 449 Lambda K H 0.320 0.137 0.394 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: 636 Number of extensions: 21 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: 459 Length adjustment: 32 Effective length of query: 393 Effective length of database: 427 Effective search space: 167811 Effective search space used: 167811 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 Ac3H11_4179 (Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19))
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.24583.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.7e-174 564.1 1.2 8.9e-174 563.9 1.2 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4179 Gamma-aminobutyrate:alpha-ketogl Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4179 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 563.9 1.2 8.9e-174 8.9e-174 2 419 .. 40 452 .. 39 453 .. 0.98 Alignments for each domain: == domain 1 score: 563.9 bits; conditional E-value: 8.9e-174 TIGR00700 2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqve 63 rr+aav++Gvg + + +++ka +ael dv+G+r+id+a+giavln+Gh h v++avk q++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4179 40 RRHAAVARGVGQAHDLFIQKARNAELWDVEGRRFIDFAGGIAVLNTGHLHAGVIAAVKAQLD 101 8************************************************************* PP TIGR00700 64 elthtafqvvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvva 125 +tht+fqvv ye yve+ e+ln++aPg+ kk++ll++Gaeavena+kiar+yt+rpgv+a lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4179 102 LYTHTCFQVVAYEPYVEVCERLNTLAPGAFAKKSLLLTTGAEAVENAIKIARAYTKRPGVIA 163 ************************************************************** PP TIGR00700 126 fsrgfhGrtnltmaltakvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiea 187 f++g+hGrtnlt+ lt+kv+PykiGfGPf++e y+a +p +++ ++ ++ l+++e lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4179 164 FTGGYHGRTNLTLGLTGKVAPYKIGFGPFPGETYHALFPNALHGVSV--EQ----ALHSVEL 219 *******************************************9988..44....55699** PP TIGR00700 188 lfvadveaeqvaavvlePvqGeGGfivpakelvaavaslckehgivliadevqtGfartGkl 249 +f+ d+e+e+vaa ++ePvqGeGGf v++ e+++ +++l ++ gi+liadevqtG rtG+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4179 220 IFKNDIEPERVAAFIVEPVQGEGGFYVAPPEFISGLKTLADRYGILLIADEVQTGAGRTGTW 281 ************************************************************** PP TIGR00700 250 faieheddkPdlitvaksladGlPlsgvvGraeildapapGglGGtyaGnPlavaaalavld 311 fa e + + Pdlit+aksla+G+Pl+gvvGra+++dapapGglGGtyaG+P+a+aa+lav++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4179 282 FASEQWPVAPDLITTAKSLAGGFPLAGVVGRADVMDAPAPGGLGGTYAGSPVACAASLAVIE 343 ************************************************************** PP TIGR00700 312 iieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelv.dpdttePdaalaek 372 +e l r++++g l+ l +l + +paigdvrglGam+a+el + d + Pdaal+++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4179 344 AFAQEKLLARSQDMGALLVRSLKDLAARIPAIGDVRGLGAMVAIELFeNGDLSRPDAALTKQ 405 *********************************************9968899********** PP TIGR00700 373 iaaaalaaGlllltaGifGniirlltPltisdelldeglkileaala 419 + a+a +Gl+ll++G +Gn+ir+l Plt sdell+egl il ++l+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4179 406 VVAEAARRGLILLSCGTHGNVIRILVPLTASDELLHEGLAILADSLE 452 *******************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (459 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: 11.75 // [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