Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate WP_085639734.1 MGEO_RS15340 4-aminobutyrate--2-oxoglutarate transaminase
Query= metacyc::MONOMER-11537 (425 letters) >NCBI__GCF_002115805.1:WP_085639734.1 Length = 460 Score = 477 bits (1227), Expect = e-139 Identities = 241/422 (57%), Positives = 307/422 (72%), Gaps = 2/422 (0%) Query: 5 NASLMKRREAAVPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKII 64 NA+L RRE AV RGVG P+FA A+NA + DVEG+ +IDFAGGIAVLNTGH HP +I Sbjct: 28 NAALWARRETAVARGVGSAAPVFAARAENAELWDVEGKRYIDFAGGIAVLNTGHRHPSVI 87 Query: 65 AAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIAR 124 AA Q + THT FQV+ YEPY+ L EK+NA PGDFAKKTLLVTTG+EAVENAVKIAR Sbjct: 88 AAAKAQEDLYTHTSFQVVPYEPYIALAEKLNALAPGDFAKKTLLVTTGAEAVENAVKIAR 147 Query: 125 AATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDS 184 A TGR GVIAFT YHGRT++TLGLTGKV PY +G P IFRA +P+ G+++ DS Sbjct: 148 AHTGRPGVIAFTAGYHGRTLLTLGLTGKVNPYKKDVGPFPSDIFRAPFPDTRAGLTVSDS 207 Query: 185 IASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQT 244 + ++E +F DA+P +AAII+EPV GEGG++ P E + LRA+CD+HGILLI+DE+Q Sbjct: 208 LRALETLFLTDAQPDRVAAIILEPVLGEGGYHPVPTEMWQALRAICDKHGILLISDEIQA 267 Query: 245 GAGRTGTFFAMEQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPI 304 G RTGT+FA+E GV DL T AKS+AGG+P+AGV G+AE MDA+ PGGLGGTY G+P+ Sbjct: 268 GFARTGTWFAIEHSGVAPDLITCAKSMAGGYPVAGVIGRAEVMDALEPGGLGGTYGGNPV 327 Query: 305 ACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPV--IGEVRALGAMIAVELFE 362 ACAAALA +E E E LL R A+G+ + I A+ + ++R LGAM+AVE Sbjct: 328 ACAAALAAIEAIESEDLLARSTALGDTMRARFADIGARVAPFRMWDIRGLGAMLAVEFVT 387 Query: 363 NGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEECF 422 + + P+ A V+A A +GLILLSCG +GN +R++VPLT+ DA +++GLAI E Sbjct: 388 DFGTATPDVALTKSVIAHALKRGLILLSCGMHGNAVRIMVPLTASDAIIEEGLAIFEAAL 447 Query: 423 AE 424 A+ Sbjct: 448 AD 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: 614 Number of extensions: 24 Number of successful extensions: 4 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: 460 Length adjustment: 32 Effective length of query: 393 Effective length of database: 428 Effective search space: 168204 Effective search space used: 168204 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_085639734.1 MGEO_RS15340 (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.667423.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-168 546.9 2.3 1.5e-168 546.7 2.3 1.0 1 NCBI__GCF_002115805.1:WP_085639734.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002115805.1:WP_085639734.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 546.7 2.3 1.5e-168 1.5e-168 2 420 .] 34 449 .. 33 449 .. 0.97 Alignments for each domain: == domain 1 score: 546.7 bits; conditional E-value: 1.5e-168 TIGR00700 2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvp 74 rr++av++Gvg +++v+aa+ae+ael dv+G+r+id+a+giavln+Gh+hP v++a k q + +tht+fqvvp NCBI__GCF_002115805.1:WP_085639734.1 34 RRETAVARGVGSAAPVFAARAENAELWDVEGKRYIDFAGGIAVLNTGHRHPSVIAAAKAQEDLYTHTSFQVVP 106 89*********************************************************************** PP TIGR00700 75 yesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPy 147 ye y++laeklna+aPg kk++l+++Gaeavenavkiar++tgrpgv+af+ g+hGrt lt+ lt+kv+Py NCBI__GCF_002115805.1:WP_085639734.1 107 YEPYIALAEKLNALAPGDFAKKTLLVTTGAEAVENAVKIARAHTGRPGVIAFTAGYHGRTLLTLGLTGKVNPY 179 ************************************************************************* PP TIGR00700 148 kiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelv 220 k GPf+++++raP+p + +++ + d l+a+e+lf +d ++++vaa++lePv GeGG+ + e+ NCBI__GCF_002115805.1:WP_085639734.1 180 KKDVGPFPSDIFRAPFPDTRA-GLT-----VSDSLRALETLFLTDAQPDRVAAIILEPVLGEGGYHPVPTEMW 246 *****************7644.444.....456788******************************99***** PP TIGR00700 221 aavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglG 293 +a++ +c++hgi+li+de+q+GfartG+ faieh ++ Pdlit aks+a+G P++gv+Grae++da +pGglG NCBI__GCF_002115805.1:WP_085639734.1 247 QALRAICDKHGILLISDEIQAGFARTGTWFAIEHSGVAPDLITCAKSMAGGYPVAGVIGRAEVMDALEPGGLG 319 ************************************************************************* PP TIGR00700 294 GtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevp..aigdvrglGamiavelv.dpdtt 363 Gty+GnP+a+aaala ++ ie+e l r+ +g ++ + ++ + v ++ d+rglGam+ave+v d +t+ NCBI__GCF_002115805.1:WP_085639734.1 320 GTYGGNPVACAAALAAIEAIESEDLLARSTALGDTMRARFADIGARVApfRMWDIRGLGAMLAVEFVtDFGTA 392 *****************************************998766434689**************99**** PP TIGR00700 364 ePdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaalad 420 Pd al++ + a+al++Gl+ll++G++Gn +r++ Plt sd++++egl i eaalad NCBI__GCF_002115805.1:WP_085639734.1 393 TPDVALTKSVIAHALKRGLILLSCGMHGNAVRIMVPLTASDAIIEEGLAIFEAALAD 449 *******************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (460 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: 17.50 // [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