Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate H281DRAFT_03179 H281DRAFT_03179 4-aminobutyrate aminotransferase apoenzyme
Query= BRENDA::Q0K2K2 (423 letters) >FitnessBrowser__Burk376:H281DRAFT_03179 Length = 429 Score = 601 bits (1549), Expect = e-176 Identities = 293/423 (69%), Positives = 343/423 (81%) Query: 1 MTMKNLELNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRH 60 M +KN EL R+ ATPRGVGVMCDFYA+RA+NA LWDVEGR + DFAAGIAV NTGHRH Sbjct: 1 MNLKNAELKSRKDAATPRGVGVMCDFYAERAQNAELWDVEGRRFIDFAAGIAVCNTGHRH 60 Query: 61 PRVMQAIAAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAI 120 P+++ AI QL+RFTHTAYQIVPY YV LAE++N P KTA FTTGAEAVENAI Sbjct: 61 PKIVAAIRDQLDRFTHTAYQIVPYASYVELAEKLNERAPGDHPKKTAFFTTGAEAVENAI 120 Query: 121 KIARAHTGRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVS 180 KIARA TGRPGVIAF+G FHGRTL+GMALTGKVAPYK GFGPFPSD++HAPFP+ LHGVS Sbjct: 121 KIARAATGRPGVIAFTGGFHGRTLMGMALTGKVAPYKAGFGPFPSDVFHAPFPNPLHGVS 180 Query: 181 TERALQALEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIAD 240 T +L+A+E LFK DIDP RVAAII EPVQGEGGF APA+F+R LR +C++HGI+LIAD Sbjct: 181 TADSLKAIEFLFKADIDPKRVAAIIFEPVQGEGGFYPAPAEFVRALRKLCNEHGILLIAD 240 Query: 241 EVQTGFGRTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYA 300 EVQTGF RTGK+FAM H+DV PDL+T+AKSLAGGMPLS V GRA +MDA PGGLGGTYA Sbjct: 241 EVQTGFARTGKLFAMHHYDVVPDLMTVAKSLAGGMPLSGVIGRADVMDAAAPGGLGGTYA 300 Query: 301 GNPLAVAAAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEF 360 GNPLAVAAA AV+D+I+EEKLCER+ LG +++ L+A + P +A+VRG G MVA EF Sbjct: 301 GNPLAVAAALAVLDIIDEEKLCERATILGDRVKAKLIALQNEAPQIADVRGPGGMVAVEF 360 Query: 361 CDPATGQPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQA 420 C P + +P AE KRVQTRAL+ GL+LL CG Y NV+RFL+PLTI FD ALA+L Sbjct: 361 CKPGSTEPDAEFTKRVQTRALKRGLLLLVCGVYSNVVRFLFPLTIEDTVFDEALAILEDV 420 Query: 421 LAE 423 + + Sbjct: 421 IKD 423 Lambda K H 0.321 0.136 0.400 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: 645 Number of extensions: 18 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: 423 Length of database: 429 Length adjustment: 32 Effective length of query: 391 Effective length of database: 397 Effective search space: 155227 Effective search space used: 155227 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 (21.9 bits) S2: 51 (24.3 bits)
Align candidate H281DRAFT_03179 H281DRAFT_03179 (4-aminobutyrate aminotransferase apoenzyme)
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.21670.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-200 650.3 0.7 6.1e-200 650.1 0.7 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_03179 H281DRAFT_03179 4-aminobutyrate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_03179 H281DRAFT_03179 4-aminobutyrate aminotransferase apoenzyme # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 650.1 0.7 6.1e-200 6.1e-200 2 420 .] 11 423 .. 10 423 .. 0.99 Alignments for each domain: == domain 1 score: 650.1 bits; conditional E-value: 6.1e-200 TIGR00700 2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelth 67 r++aa+++Gvgv+++++a +a++ael dv+G+r+id+aagiav n+Gh+hPk+v+a++ q++++th lcl|FitnessBrowser__Burk376:H281DRAFT_03179 11 RKDAATPRGVGVMCDFYAERAQNAELWDVEGRRFIDFAAGIAVCNTGHRHPKIVAAIRDQLDRFTH 76 899*************************************************************** PP TIGR00700 68 tafqvvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGr 133 ta+q+vpy syvelaekln+ aPg ++kk++++++Gaeavena+kiar+ tgrpgv+af++gfhGr lcl|FitnessBrowser__Burk376:H281DRAFT_03179 77 TAYQIVPYASYVELAEKLNERAPGDHPKKTAFFTTGAEAVENAIKIARAATGRPGVIAFTGGFHGR 142 ****************************************************************** PP TIGR00700 134 tnltmaltakvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqva 199 t + malt+kv+Pyk GfGPf+++v++aP+p ++++ ++ d l+aie lf+ad+++++va lcl|FitnessBrowser__Burk376:H281DRAFT_03179 143 TLMGMALTGKVAPYKAGFGPFPSDVFHAPFPNPLHGVST------ADSLKAIEFLFKADIDPKRVA 202 ************************************999......34677**************** PP TIGR00700 200 avvlePvqGeGGfivpakelvaavaslckehgivliadevqtGfartGklfaieheddkPdlitva 265 a+++ePvqGeGGf ++ e+v a+++lc+ehgi+liadevqtGfartGklfa++h+d++Pdl+tva lcl|FitnessBrowser__Burk376:H281DRAFT_03179 203 AIIFEPVQGEGGFYPAPAEFVRALRKLCNEHGILLIADEVQTGFARTGKLFAMHHYDVVPDLMTVA 268 ****************************************************************** PP TIGR00700 266 ksladGlPlsgvvGraeildapapGglGGtyaGnPlavaaalavldiieeeglieraeqigklvkd 331 ksla+G+Plsgv+Gra+++da+apGglGGtyaGnPlavaaalavldii+ee l+era +g +vk lcl|FitnessBrowser__Burk376:H281DRAFT_03179 269 KSLAGGMPLSGVIGRADVMDAAAPGGLGGTYAGNPLAVAAALAVLDIIDEEKLCERATILGDRVKA 334 ****************************************************************** PP TIGR00700 332 klielkeevpaigdvrglGamiavelvdpdttePdaalaekiaaaalaaGlllltaGifGniirll 397 kli l++e p+i+dvrg G m+ave+ +p++tePda +++++++al++Gllll +G++ n++r+l lcl|FitnessBrowser__Burk376:H281DRAFT_03179 335 KLIALQNEAPQIADVRGPGGMVAVEFCKPGSTEPDAEFTKRVQTRALKRGLLLLVCGVYSNVVRFL 400 ****************************************************************** PP TIGR00700 398 tPltisdelldeglkileaalad 420 Plti d+ +de+l ile++++d lcl|FitnessBrowser__Burk376:H281DRAFT_03179 401 FPLTIEDTVFDEALAILEDVIKD 423 *******************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (429 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: 10.54 // [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