Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate HSERO_RS03330 HSERO_RS03330 branched-chain amino acid aminotransferase
Query= BRENDA::P0AB80 (309 letters) >FitnessBrowser__HerbieS:HSERO_RS03330 Length = 306 Score = 278 bits (712), Expect = 9e-80 Identities = 140/299 (46%), Positives = 195/299 (65%), Gaps = 2/299 (0%) Query: 9 IWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKIY 68 IW +GE++ W DA VHV++H LHYG VFEG+R Y + G +FR +EH +RL +SAKI+ Sbjct: 10 IWKDGELIDWRDATVHVLTHTLHYGMGVFEGVRAYKTPDGTAIFRLQEHTRRLRNSAKIF 69 Query: 69 RFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAAFPWG 128 + V D L +A R V+R+N L S YIRPLI++G +GV+ G V +AA+ WG Sbjct: 70 QMEVPYDHDTLAQAQRQVVRENQLESCYIRPLIWIGSEKLGVS-AKGNQIHVAVAAWSWG 128 Query: 129 AYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIALDV 188 AYLG + L +GI SS++R N AKA G Y++S+L EA GY E + LD Sbjct: 129 AYLGEDGLNKGIRVKTSSFSRHHVNVSLVRAKACGYYINSILANQEALADGYDEALLLDT 188 Query: 189 NGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRESLY 248 GY+SEG+GEN+F VK+G ++TP +S L GITRDA++ +A++LGIEV E+ ++R+ +Y Sbjct: 189 EGYVSEGSGENVFIVKNGKIYTPDL-ASCLDGITRDAVLTMARDLGIEVIEKRITRDEMY 247 Query: 249 LADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDKWGWLDQV 307 ADE F +GTAAEITP+R +D +G G GPVT+++Q FF + G WL V Sbjct: 248 CADEAFFTGTAAEITPIRELDRRVIGSGARGPVTEKLQTLFFDVVAGRAPQYKHWLTLV 306 Lambda K H 0.319 0.136 0.413 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: 299 Number of extensions: 13 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: 309 Length of database: 306 Length adjustment: 27 Effective length of query: 282 Effective length of database: 279 Effective search space: 78678 Effective search space used: 78678 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: 48 (23.1 bits)
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