Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate HSERO_RS09025 HSERO_RS09025 GntR family transcriptional regulator
Query= BRENDA::A0A060PQX5 (417 letters) >FitnessBrowser__HerbieS:HSERO_RS09025 Length = 500 Score = 154 bits (388), Expect = 8e-42 Identities = 110/344 (31%), Positives = 165/344 (47%), Gaps = 14/344 (4%) Query: 51 GGLPAPETFPVEIIAEITKEVLEKHAAQALQYGTTKGFTPLRLALAEWMRKRYDIPISKV 110 GGL P+ E+IA + V + L YGT +GF PLR L + +I + Sbjct: 149 GGLLPPDWLDGELIANALRAVSRDNPQLLLGYGTPQGFLPLRQQL-QLKLAELEIAAAPE 207 Query: 111 DIMITSGSQQALDLIGRVFINPGDIVVVEAPTYLAALQAFKYYEPEFVQIPLDDEGMRVD 170 I++T+G Q LD + R F+ PGD++ V+ P + +F + V IP +G + Sbjct: 208 QIVLTTGVTQGLDTVARHFLRPGDVIFVDDPAWFLMFGSFAALGAKVVGIPRLGDGPDI- 266 Query: 171 LLEEKLQELEKEGKKVKLVYTIPTFQNPAGVTMSEKRRKRLLELASEYDFLIVEDNPYGE 230 +L+EL K KL NP ++S + ++L +A E+DF+IVED+ Y + Sbjct: 267 ---ARLRELAAVHKP-KLYVINSVLHNPTSTSLSAAKAFQVLRIAEEHDFVIVEDDIYCD 322 Query: 231 LRYSGEPVKP---IKAWDDEGRVMYLGTFSKILAPGFRIGWIAAEPHLIRKLEIAKQSVD 287 + + G V+P I A D RV+YLG FSK L+ R+G+IA L R L K Sbjct: 323 M-HPGSAVQPATRIAALDQLQRVIYLGGFSKTLSANLRVGYIATSAELARSLADRKLLST 381 Query: 288 LCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPRRDAMLKALEEFMPEGVRWTKPEGGMF 347 L T + +A+K + GH H + RD +++ LE + V P GMF Sbjct: 382 LTTGEIGERVAYKVLSEGHYRKHAERVRARLNGARDKVMRQLERLGMDVVE--APPCGMF 439 Query: 348 VWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHRDVKNTMRLN 391 +WV G DT +M E A+ +G PG F + MR+N Sbjct: 440 LWV--DTGRDTNVMTEAAMQEGFLLAPGSLFSPAQLPSTYMRIN 481 Lambda K H 0.318 0.137 0.398 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: 449 Number of extensions: 21 Number of successful extensions: 5 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: 417 Length of database: 500 Length adjustment: 33 Effective length of query: 384 Effective length of database: 467 Effective search space: 179328 Effective search space used: 179328 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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