Align 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 (characterized)
to candidate BWI76_RS26375 BWI76_RS26375 aspartate aminotransferase family protein
Query= SwissProt::P50457 (421 letters) >FitnessBrowser__Koxy:BWI76_RS26375 Length = 421 Score = 651 bits (1679), Expect = 0.0 Identities = 317/419 (75%), Positives = 362/419 (86%) Query: 1 MSNNEFHQRRLSATPRGVGVMCNFFAQSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPD 60 M ++E +QRR ATPRGVGVMC++F + AENATL D+EGNE IDFAAGIAVLNTGHRHP Sbjct: 1 MKSSELNQRRQQATPRGVGVMCSYFVEKAENATLWDIEGNEVIDFAAGIAVLNTGHRHPK 60 Query: 61 LVAAVEQQLQQFTHTAYQIVPYESYVTLAEKINALAPVSGQAKTAFFTTGAEAVENAVKI 120 ++AAVEQQLQ FTHTAYQIVPYESYVTLAE+INALAP+ G AKTAFFTTGAEAVENAVKI Sbjct: 61 IIAAVEQQLQAFTHTAYQIVPYESYVTLAERINALAPIDGPAKTAFFTTGAEAVENAVKI 120 Query: 121 ARAHTGRPGVIAFSGGFHGRTYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQ 180 ARA+TGRPG+I F GGFHGRT+MTMALTGKVAPYKIGFGPFPGSVYH YP+ HGI+T Sbjct: 121 ARAYTGRPGLITFGGGFHGRTFMTMALTGKVAPYKIGFGPFPGSVYHAVYPNAAHGITTA 180 Query: 181 DSLDAIERLFKSDIEAKQVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEV 240 D++ +++R+FK+DI A QVAAI+ EP+QGEGGFNVAP E + A+R LCD HGI++IADEV Sbjct: 181 DAMKSLDRIFKADIAADQVAAIVLEPIQGEGGFNVAPPEFMQALRALCDTHGILLIADEV 240 Query: 241 QSGFARTGKLFAMDHYADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGN 300 Q+GFARTGKLFAM HY KPDLMTMAKSLAGG PLSGVVG A +MDAPAPGGLGGTYAGN Sbjct: 241 QTGFARTGKLFAMQHYDVKPDLMTMAKSLAGGFPLSGVVGRAEVMDAPAPGGLGGTYAGN 300 Query: 301 PLAVAAAHAVLNIIDKESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFND 360 PLAVAAAHAVL++I++E LC+RA +LG LK L A++S PAIA VRG GSM+AVEFND Sbjct: 301 PLAVAAAHAVLDVIEEEQLCQRAERLGSHLKEVLNQARQSCPAIADVRGQGSMVAVEFND 360 Query: 361 PQTGEPSAAIAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDAL 419 PQTGEPSA I ++IQQ+A GLLLL+CG YGNVIRFLYPLTIPDAQF A+ IL L Sbjct: 361 PQTGEPSAEITRQIQQKAQENGLLLLSCGVYGNVIRFLYPLTIPDAQFTKALDILARVL 419 Lambda K H 0.319 0.134 0.388 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: 658 Number of extensions: 17 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: 421 Length of database: 421 Length adjustment: 32 Effective length of query: 389 Effective length of database: 389 Effective search space: 151321 Effective search space used: 151321 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: 50 (23.9 bits)
Align candidate BWI76_RS26375 BWI76_RS26375 (aspartate aminotransferase family protein)
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.18206.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-207 675.3 3.0 1.5e-207 675.2 3.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS26375 BWI76_RS26375 aspartate aminotra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS26375 BWI76_RS26375 aspartate aminotransferase family protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 675.2 3.0 1.5e-207 1.5e-207 1 418 [. 8 419 .. 8 421 .] 0.99 Alignments for each domain: == domain 1 score: 675.2 bits; conditional E-value: 1.5e-207 TIGR00700 1 qrraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafq 71 qrr++a+++Gvgv++++++ kae+a+l d++Gn+ id+aagiavln+Gh+hPk+++av++q++ +thta+q lcl|FitnessBrowser__Koxy:BWI76_RS26375 8 QRRQQATPRGVGVMCSYFVEKAENATLWDIEGNEVIDFAAGIAVLNTGHRHPKIIAAVEQQLQAFTHTAYQ 78 89********************************************************************* PP TIGR00700 72 vvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmalta 142 +vpyesyv+lae++na+aP g++k++++++Gaeavenavkiar+ytgrpg+++f +gfhGrt++tmalt+ lcl|FitnessBrowser__Koxy:BWI76_RS26375 79 IVPYESYVTLAERINALAPIDGPAKTAFFTTGAEAVENAVKIARAYTGRPGLITFGGGFHGRTFMTMALTG 149 *********************************************************************** PP TIGR00700 143 kvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfi 213 kv+PykiGfGPf+++vy+a +p ++i++ d +++++++f+ad++a+qvaa+vleP+qGeGGf+ lcl|FitnessBrowser__Koxy:BWI76_RS26375 150 KVAPYKIGFGPFPGSVYHAVYPNAAHGITT------ADAMKSLDRIFKADIAADQVAAIVLEPIQGEGGFN 214 ***************************998......3456799**************************** PP TIGR00700 214 vpakelvaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeil 284 v++ e+++a++ lc+ hgi+liadevqtGfartGklfa++h+d+kPdl+t+aksla+G+PlsgvvGrae++ lcl|FitnessBrowser__Koxy:BWI76_RS26375 215 VAPPEFMQALRALCDTHGILLIADEVQTGFARTGKLFAMQHYDVKPDLMTMAKSLAGGFPLSGVVGRAEVM 285 *********************************************************************** PP TIGR00700 285 dapapGglGGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiav 355 dapapGglGGtyaGnPlavaaa+avld+ieee l++rae++g +k+ l +++++ pai+dvrg+G+m+av lcl|FitnessBrowser__Koxy:BWI76_RS26375 286 DAPAPGGLGGTYAGNPLAVAAAHAVLDVIEEEQLCQRAERLGSHLKEVLNQARQSCPAIADVRGQGSMVAV 356 *********************************************************************** PP TIGR00700 356 elvdpdttePdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaal 418 e++dp+t+eP+a ++++i+++a+++Gllll++G++Gn+ir+l+Plti+d+++ ++l+il +l lcl|FitnessBrowser__Koxy:BWI76_RS26375 357 EFNDPQTGEPSAEITRQIQQKAQENGLLLLSCGVYGNVIRFLYPLTIPDAQFTKALDILARVL 419 ***********************************************************9887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (421 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 8.81 // [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