Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate Pf1N1B4_1733 5-aminovalerate aminotransferase (EC 2.6.1.48) / Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Query= metacyc::MONOMER-11537 (425 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1733 Length = 425 Score = 820 bits (2119), Expect = 0.0 Identities = 416/425 (97%), Positives = 421/425 (99%) Query: 1 MSKTNASLMKRREAAVPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVH 60 MSKTNASLMKRREAAVPRGVGQIHPIFA+SAKNATVTDVEGREFIDFAGGIAVLNTGHVH Sbjct: 1 MSKTNASLMKRREAAVPRGVGQIHPIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVH 60 Query: 61 PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV 120 PKIIAAVTEQLNKLTHTCFQVLAYEPYVE+CEKINAKVPGDFAKKTLLVTTGSEAVEN++ Sbjct: 61 PKIIAAVTEQLNKLTHTCFQVLAYEPYVEVCEKINAKVPGDFAKKTLLVTTGSEAVENSI 120 Query: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS 180 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS Sbjct: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS 180 Query: 181 IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD 240 IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD Sbjct: 181 IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD 240 Query: 241 EVQTGAGRTGTFFAMEQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA 300 EVQTGAGRTGTFFAMEQMGV ADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA Sbjct: 241 EVQTGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA 300 Query: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL 360 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL Sbjct: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL 360 Query: 361 FENGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEE 420 F +GDSHKPNAAAVA VVAKARDKGLILLSCGTYGNVLRVLVPLTSPD QLDKGLAIIEE Sbjct: 361 FVDGDSHKPNAAAVASVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDEQLDKGLAIIEE 420 Query: 421 CFAEL 425 CFAEL Sbjct: 421 CFAEL 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: 827 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: 425 Length adjustment: 32 Effective length of query: 393 Effective length of database: 393 Effective search space: 154449 Effective search space used: 154449 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 Pf1N1B4_1733 (5-aminovalerate aminotransferase (EC 2.6.1.48) / 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.12879.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.8e-166 537.5 7.4 1e-165 537.4 7.4 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1733 5-aminovalerate aminotransferase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1733 5-aminovalerate aminotransferase (EC 2.6.1.48) / Gamma-aminobutyrate:a # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 537.4 7.4 1e-165 1e-165 1 418 [. 10 422 .. 10 424 .. 0.99 Alignments for each domain: == domain 1 score: 537.4 bits; conditional E-value: 1e-165 TIGR00700 1 qrraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqvee 64 +rr+aav++Gvg +++a +a++a++ dv+G+++id+a+giavln+Gh hPk+++av +q+++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1733 10 KRREAAVPRGVGQIHPIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNK 73 69************************************************************** PP TIGR00700 65 lthtafqvvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsr 128 ltht+fqv+ ye yve+ ek+na Pg kk++l+++G+eaven++kiar+ tgr gv+af++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1733 74 LTHTCFQVLAYEPYVEVCEKINAKVPGDFAKKTLLVTTGSEAVENSIKIARAATGRAGVIAFTG 137 **************************************************************** PP TIGR00700 129 gfhGrtnltmaltakvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvad 192 ++hGrt +t+ lt+kv Py G+G +++ ++ra +p ++++ + dd +a+ie++f+ d lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1733 138 AYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSI------DDSIASIERIFKND 195 ****************************************9877......88899********* PP TIGR00700 193 veaeqvaavvlePvqGeGGfivpakelvaavaslckehgivliadevqtGfartGklfaiehed 256 e++++aa+++ePvqGeGGf v++ke+++ ++ lc++hgi+liadevqtG rtG++fa+e ++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1733 196 AEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQMG 259 **************************************************************** PP TIGR00700 257 dkPdlitvaksladGlPlsgvvGraeildapapGglGGtyaGnPlavaaalavldiieeeglie 320 + dl t aks+a+G+Pl+gv G+ae +da apGglGGtyaG+P+a+aaalav+++ eee l + lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1733 260 VAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEVFEEEHLLD 323 **************************************************************** PP TIGR00700 321 raeqigklvkdklielkeevpaigdvrglGamiavelv.dpdttePdaalaekiaaaalaaGll 383 r++ +g+++ l ++++ p+ig+vr lGamiavel d d+++P+aa + + a+a+ +Gl+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1733 324 RCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFvDGDSHKPNAAAVASVVAKARDKGLI 387 ************************************866************************* PP TIGR00700 384 lltaGifGniirlltPltisdelldeglkileaal 418 ll++G +Gn++r+l Plt +de+ld+gl i+e+ + lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1733 388 LLSCGTYGNVLRVLVPLTSPDEQLDKGLAIIEECF 422 *******************************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (425 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: 9.46 // [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