Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate GFF3586 Psest_3653 4-aminobutyrate aminotransferase, prokaryotic type
Query= metacyc::MONOMER-11537 (425 letters) >FitnessBrowser__psRCH2:GFF3586 Length = 426 Score = 727 bits (1877), Expect = 0.0 Identities = 366/425 (86%), Positives = 393/425 (92%) Query: 1 MSKTNASLMKRREAAVPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVH 60 MSKTN SLM+RR AAVPRGVGQIHPIFAD AKN++V DVEGREFIDFAGGIAVLNTGH+H Sbjct: 1 MSKTNESLMQRRVAAVPRGVGQIHPIFADHAKNSSVVDVEGREFIDFAGGIAVLNTGHLH 60 Query: 61 PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV 120 PKII AV +QL+KLTHTCFQVLAYEPYVELCEKINA+VPGDFAKKTLLVTTGSEAVENAV Sbjct: 61 PKIIKAVEDQLHKLTHTCFQVLAYEPYVELCEKINARVPGDFAKKTLLVTTGSEAVENAV 120 Query: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS 180 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKV PYSAGMGLMPGGIFRALYP ++GVS Sbjct: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVAPYSAGMGLMPGGIFRALYPCAIYGVS 180 Query: 181 IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD 240 +DDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGF VAPK+FM RLRALCD+HGILLIAD Sbjct: 181 VDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFNVAPKDFMARLRALCDEHGILLIAD 240 Query: 241 EVQTGAGRTGTFFAMEQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA 300 EVQTGAGRTGTFFAMEQMGV ADLTTFAKS+ GGFP+AGVCGKAE MDAIAPGGLGGTYA Sbjct: 241 EVQTGAGRTGTFFAMEQMGVVADLTTFAKSVGGGFPIAGVCGKAEIMDAIAPGGLGGTYA 300 Query: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL 360 G+P++CAAALAV+EVFEEE LLDRCKAV ERL TGLKAIQ K+ IGEVR LGAMIA+EL Sbjct: 301 GNPLSCAAALAVLEVFEEEKLLDRCKAVAERLTTGLKAIQTKHKEIGEVRGLGAMIAIEL 360 Query: 361 FENGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEE 420 FE+GD +P AA +Q+VA+ARDKGLILLSCGTY NVLRVLVPLT+ D LD+GLAII E Sbjct: 361 FEDGDHARPAAALTSQIVARARDKGLILLSCGTYYNVLRVLVPLTAEDELLDRGLAIIGE 420 Query: 421 CFAEL 425 CF EL Sbjct: 421 CFDEL 425 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: 748 Number of extensions: 19 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: 426 Length adjustment: 32 Effective length of query: 393 Effective length of database: 394 Effective search space: 154842 Effective search space used: 154842 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 GFF3586 Psest_3653 (4-aminobutyrate aminotransferase, prokaryotic type)
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.2193196.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-163 530.4 5.1 1.5e-163 530.2 5.1 1.0 1 FitnessBrowser__psRCH2:GFF3586 Domain annotation for each sequence (and alignments): >> FitnessBrowser__psRCH2:GFF3586 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 530.2 5.1 1.5e-163 1.5e-163 1 416 [. 10 420 .. 10 424 .. 0.98 Alignments for each domain: == domain 1 score: 530.2 bits; conditional E-value: 1.5e-163 TIGR00700 1 qrraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvpyesyv 79 qrr aav++Gvg +++a +a+++ + dv+G+++id+a+giavln+Gh hPk+++av+ q+++ltht+fqv+ ye yv FitnessBrowser__psRCH2:GFF3586 10 QRRVAAVPRGVGQIHPIFADHAKNSSVVDVEGREFIDFAGGIAVLNTGHLHPKIIKAVEDQLHKLTHTCFQVLAYEPYV 88 89***************************************************************************** PP TIGR00700 80 elaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPykiGfGPfapev 158 el ek+na Pg kk++l+++G+eavenavkiar+ tgr gv+af++++hGrt +t+ lt+kv+Py G+G +++ + FitnessBrowser__psRCH2:GFF3586 89 ELCEKINARVPGDFAKKTLLVTTGSEAVENAVKIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVAPYSAGMGLMPGGI 167 ******************************************************************************* PP TIGR00700 159 yraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelvaavaslckehgivliad 237 +ra +p + + ++ dd +a+ie++f+ d e++++aa+++ePvqGeGGf+v++k+++a ++ lc+ehgi+liad FitnessBrowser__psRCH2:GFF3586 168 FRALYPCAIYGVSV------DDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFNVAPKDFMARLRALCDEHGILLIAD 240 ******99887766......88999****************************************************** PP TIGR00700 238 evqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglGGtyaGnPlavaaalavldiieee 316 evqtG rtG++fa+e ++++ dl t aks+ +G+P++gv G+aei+da apGglGGtyaGnPl++aaalavl++ eee FitnessBrowser__psRCH2:GFF3586 241 EVQTGAGRTGTFFAMEQMGVVADLTTFAKSVGGGFPIAGVCGKAEIMDAIAPGGLGGTYAGNPLSCAAALAVLEVFEEE 319 ******************************************************************************* PP TIGR00700 317 glieraeqigklvkdklielkeevpaigdvrglGamiavelv.dpdttePdaalaekiaaaalaaGlllltaGifGnii 394 l +r++ + ++++ l ++ + + ig+vrglGamia+el d d + P aal+ +i a+a+ +Gl+ll++G + n++ FitnessBrowser__psRCH2:GFF3586 320 KLLDRCKAVAERLTTGLKAIQTKHKEIGEVRGLGAMIAIELFeDGDHARPAAALTSQIVARARDKGLILLSCGTYYNVL 398 ****************************************998999********************************* PP TIGR00700 395 rlltPltisdelldeglkilea 416 r+l Plt delld gl i+ + FitnessBrowser__psRCH2:GFF3586 399 RVLVPLTAEDELLDRGLAIIGE 420 *******************976 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 19.48 // [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