Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_068170823.1 HTA01S_RS10480 4-aminobutyrate--2-oxoglutarate transaminase
Query= BRENDA::Q0K2K2 (423 letters) >NCBI__GCF_001592305.1:WP_068170823.1 Length = 428 Score = 548 bits (1412), Expect = e-160 Identities = 276/419 (65%), Positives = 328/419 (78%), Gaps = 3/419 (0%) Query: 5 NLELNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVM 64 N +QRR ATPRGVGVM DF+ D A+NA LWD+EGR + DFA GIAVLNTGH HP+V Sbjct: 10 NAAWHQRRLDATPRGVGVMGDFFIDHAKNAELWDIEGRRFIDFAGGIAVLNTGHVHPKVQ 69 Query: 65 QAIAAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKIAR 124 AIAAQL+RFTH+ YQ+VPY YV+LAERINA+VPI+G KTA F+TGAEA+ENAIKIAR Sbjct: 70 AAIAAQLQRFTHSCYQVVPYAEYVSLAERINAIVPIEGKAKTAFFSTGAEAIENAIKIAR 129 Query: 125 AHTGRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERA 184 + TGR GVIAF GAFHGR+L ++LTGKV PYK GFGPFP +IYH PFP+ G S + Sbjct: 130 SSTGRSGVIAFGGAFHGRSLFAVSLTGKVQPYKAGFGPFPPEIYHVPFPA--EGASLDET 187 Query: 185 LQALEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQT 244 +A++ +FK DI+P+RVAAI+ EPVQGEGGF D + LRA+CDQHGI+LIADEVQT Sbjct: 188 KRAMDHVFKCDIEPSRVAAIVFEPVQGEGGFNPIQKDAVLWLRALCDQHGILLIADEVQT 247 Query: 245 GFGRTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPL 304 GF RTG+MFAM H+ V PDL+TMAKS+AGG LSAVSG+AAIMD P PGGLGGTYAGNPL Sbjct: 248 GFARTGRMFAMEHYGVSPDLMTMAKSMAGGTTLSAVSGKAAIMDGPAPGGLGGTYAGNPL 307 Query: 305 AVAAAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCDPA 364 A+AA+HAV+DV+ EEKL ER+ LG QL HL A + P + EVRGLG+MVA EF D A Sbjct: 308 AIAASHAVLDVMAEEKLPERAQRLGDQLVAHLRAAKAKYPRIGEVRGLGAMVACEFVD-A 366 Query: 365 TGQPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQALAE 423 G P A+ K+VQ AL+ GL+LLTCG YGNVIR+L+PLTI + F AL VL A+AE Sbjct: 367 AGAPDADTTKQVQAAALKRGLLLLTCGVYGNVIRYLFPLTIEDSVFAEALGVLDAAMAE 425 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: 627 Number of extensions: 23 Number of successful extensions: 3 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: 428 Length adjustment: 32 Effective length of query: 391 Effective length of database: 396 Effective search space: 154836 Effective search space used: 154836 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 WP_068170823.1 HTA01S_RS10480 (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.1747470.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-176 573.1 2.5 1.7e-176 572.9 2.5 1.0 1 NCBI__GCF_001592305.1:WP_068170823.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001592305.1:WP_068170823.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 572.9 2.5 1.7e-176 1.7e-176 1 419 [. 15 424 .. 15 425 .. 0.98 Alignments for each domain: == domain 1 score: 572.9 bits; conditional E-value: 1.7e-176 TIGR00700 1 qrraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvv 73 qrr+ a+++Gvgv+ ++++ +a++ael d++G+r+id+a+giavln+Gh hPkv +a+ q++++th+++qvv NCBI__GCF_001592305.1:WP_068170823.1 15 QRRLDATPRGVGVMGDFFIDHAKNAELWDIEGRRFIDFAGGIAVLNTGHVHPKVQAAIAAQLQRFTHSCYQVV 87 89*********************************************************************** PP TIGR00700 74 pyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkP 146 py yv+lae++nai P g++k++++++Gaea+ena+kiar+ tgr gv+af ++fhGr+ ++++lt+kv+P NCBI__GCF_001592305.1:WP_068170823.1 88 PYAEYVSLAERINAIVPIEGKAKTAFFSTGAEAIENAIKIARSSTGRSGVIAFGGAFHGRSLFAVSLTGKVQP 160 ************************************************************************* PP TIGR00700 147 ykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakel 219 yk GfGPf+pe+y++P+p + sld+ +a++++f+ d+e+ +vaa+v+ePvqGeGGf+ k+ NCBI__GCF_001592305.1:WP_068170823.1 161 YKAGFGPFPPEIYHVPFPAE--------GASLDETKRAMDHVFKCDIEPSRVAAIVFEPVQGEGGFNPIQKDA 225 *****************975........245677778************************************ PP TIGR00700 220 vaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGgl 292 v ++ lc++hgi+liadevqtGfartG++fa+eh+++ Pdl+t+aks+a+G ls+v G+a i+d papGgl NCBI__GCF_001592305.1:WP_068170823.1 226 VLWLRALCDQHGILLIADEVQTGFARTGRMFAMEHYGVSPDLMTMAKSMAGGTTLSAVSGKAAIMDGPAPGGL 298 ************************************************************************* PP TIGR00700 293 GGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelvdpdtteP 365 GGtyaGnPla+aa++avld++ ee l era+++g + +l +k++ p+ig+vrglGam+a e+vd+ ++ P NCBI__GCF_001592305.1:WP_068170823.1 299 GGTYAGNPLAIAASHAVLDVMAEEKLPERAQRLGDQLVAHLRAAKAKYPRIGEVRGLGAMVACEFVDA-AGAP 370 ******************************************************************97.578* PP TIGR00700 366 daalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaala 419 da +++++aaal++Gllllt+G++Gn+ir+l Plti d+ + e+l +l aa+a NCBI__GCF_001592305.1:WP_068170823.1 371 DADTTKQVQAAALKRGLLLLTCGVYGNVIRYLFPLTIEDSVFAEALGVLDAAMA 424 **************************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (428 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 17.08 // [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