Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_015887459.1 NGR_RS06525 4-aminobutyrate--2-oxoglutarate transaminase
Query= BRENDA::Q0K2K2 (423 letters) >NCBI__GCF_000018545.1:WP_015887459.1 Length = 422 Score = 546 bits (1406), Expect = e-160 Identities = 268/416 (64%), Positives = 319/416 (76%) Query: 8 LNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAI 67 L R+ A RGVG+ YADRAENA +WD E Y DFAAGIAV+NTGHRHP+V+ A+ Sbjct: 4 LTDRKNAAISRGVGMTTQIYADRAENAEIWDKESNRYIDFAAGIAVVNTGHRHPKVIAAV 63 Query: 68 AAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKIARAHT 127 AQL+RFTHT +Q+VPY+ YV LAER+NAL P + KT TTGAEAVENA+KIARA T Sbjct: 64 KAQLDRFTHTCHQVVPYENYVHLAERLNALAPGKFAKKTIFVTTGAEAVENAVKIARAAT 123 Query: 128 GRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQA 187 GR VIAF G FHGRT +GMALTGKV PYK+GFG P+D++HAPFP LHGVS E++L A Sbjct: 124 GRQAVIAFGGGFHGRTFMGMALTGKVVPYKVGFGAMPADVFHAPFPIELHGVSVEQSLAA 183 Query: 188 LEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFG 247 L+ LF D+DP RVAAII+EPVQGEGGF AP FM+ LR +CDQHGI+LIADEVQTGF Sbjct: 184 LKKLFAADVDPGRVAAIILEPVQGEGGFYPAPTAFMKALREICDQHGILLIADEVQTGFA 243 Query: 248 RTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVA 307 RTGK+FAM HHDV PDL+TMAKSLAGG PL+AV+GRA IMDAP PGGLGGTY GNP+ +A Sbjct: 244 RTGKLFAMEHHDVAPDLMTMAKSLAGGFPLAAVTGRAEIMDAPGPGGLGGTYGGNPIGIA 303 Query: 308 AAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCDPATGQ 367 AAHAV+DVIEEE+LCER+ LG +L++ L R+ P + ++RG G M A EF D T Sbjct: 304 AAHAVLDVIEEEQLCERANQLGNRLKQRLAQIREKAPEIVDIRGPGFMNAVEFNDVKTKL 363 Query: 368 PSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQALAE 423 PSAE A +V+ ALE GL+LLTCG +GNVIRFL P+TI F AL +L ++ E Sbjct: 364 PSAEFANKVRLIALEKGLILLTCGVHGNVIRFLAPITIQDEVFAEALDILEASILE 419 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: 603 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: 422 Length adjustment: 32 Effective length of query: 391 Effective length of database: 390 Effective search space: 152490 Effective search space used: 152490 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: 50 (23.9 bits)
Align candidate WP_015887459.1 NGR_RS06525 (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.1389006.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-187 609.0 5.5 2.2e-187 608.7 5.5 1.0 1 NCBI__GCF_000018545.1:WP_015887459.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000018545.1:WP_015887459.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 608.7 5.5 2.2e-187 2.2e-187 2 418 .. 7 417 .. 6 419 .. 0.99 Alignments for each domain: == domain 1 score: 608.7 bits; conditional E-value: 2.2e-187 TIGR00700 2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvp 74 r++aa+s+Gvg+t++++a +ae+ae+ d + nr+id+aagiav+n+Gh+hPkv++avk q++++tht++qvvp NCBI__GCF_000018545.1:WP_015887459.1 7 RKNAAISRGVGMTTQIYADRAENAEIWDKESNRYIDFAAGIAVVNTGHRHPKVIAAVKAQLDRFTHTCHQVVP 79 7899********************************************************************* PP TIGR00700 75 yesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPy 147 ye yv+lae+lna+aPg kk++++++Gaeavenavkiar+ tgr++v+af +gfhGrt++ malt+kv Py NCBI__GCF_000018545.1:WP_015887459.1 80 YENYVHLAERLNALAPGKFAKKTIFVTTGAEAVENAVKIARAATGRQAVIAFGGGFHGRTFMGMALTGKVVPY 152 ************************************************************************* PP TIGR00700 148 kiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelv 220 k+GfG ++++v++aP+p ++++ ++ ++ laa+++lf adv++ +vaa++lePvqGeGGf ++ ++ NCBI__GCF_000018545.1:WP_015887459.1 153 KVGFGAMPADVFHAPFPIELHGVSV------EQSLAALKKLFAADVDPGRVAAIILEPVQGEGGFYPAPTAFM 219 *********************9988......45677************************************* PP TIGR00700 221 aavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglG 293 +a++++c++hgi+liadevqtGfartGklfa+eh+d+ Pdl+t+aksla+G+Pl++v+Graei+dap pGglG NCBI__GCF_000018545.1:WP_015887459.1 220 KALREICDQHGILLIADEVQTGFARTGKLFAMEHHDVAPDLMTMAKSLAGGFPLAAVTGRAEIMDAPGPGGLG 292 ************************************************************************* PP TIGR00700 294 GtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelvdpdttePd 366 Gty+GnP+++aaa+avld+ieee l+era+q+g+++k++l +++e+ p i d+rg G m ave++d +t+ P+ NCBI__GCF_000018545.1:WP_015887459.1 293 GTYGGNPIGIAAAHAVLDVIEEEQLCERANQLGNRLKQRLAQIREKAPEIVDIRGPGFMNAVEFNDVKTKLPS 365 ************************************************************************* PP TIGR00700 367 aalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaal 418 a a+k+ al++Gl+llt+G++Gn+ir+l+P+ti de + e+l+ilea++ NCBI__GCF_000018545.1:WP_015887459.1 366 AEFANKVRLIALEKGLILLTCGVHGNVIRFLAPITIQDEVFAEALDILEASI 417 ************************************************9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (422 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: 00:00:00.01 # Mc/sec: 16.26 // [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