Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate 208464 DVU2953 transcriptional regulator, GntR family
Query= BRENDA::A0A060PQX5 (417 letters) >MicrobesOnline__882:208464 Length = 520 Score = 220 bits (561), Expect = 7e-62 Identities = 126/366 (34%), Positives = 195/366 (53%), Gaps = 7/366 (1%) Query: 47 ISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQYGTTKGFTPLRLALAEWMRKRYDIP 106 I+LA G FP+ + VL + +AL+Y G+ PLR +A + + +P Sbjct: 151 IALASGNSDARLFPLASFRRTLRTVLARDGIKALEYEDPAGYAPLRRTIARILADQ-GVP 209 Query: 107 ISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAPTYLAALQAFKYYEPEFVQIPLDDEG 166 + +++T+GSQQAL L+ +V + PGD V VE P+Y + F+ V + D EG Sbjct: 210 ATPDTVLVTAGSQQALHLVAQVVLKPGDPVYVETPSYADGMALFRTLGLRIVPVFTDSEG 269 Query: 167 MRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGVTMSEKRRKRLLELASEYDFLIVEDN 226 M + L E + + G LV+T+P FQNP G+ MS +RR+R+ +A + I+ED+ Sbjct: 270 MSAEGLREAIA---RHGHG--LVFTMPNFQNPTGICMSGQRRRRIAAIAVAHGVPILEDD 324 Query: 227 PYGELRYSGEPVKPIKAWDDEGRVMYLGTFSKILAPGFRIGWIAAEPHLIRKLEIAKQSV 286 G++RY G + + G Y GTFSK+L PG R+G++ AE ++R L K+ Sbjct: 325 YVGDIRYEGYSQPSLHSLTPPGHTFYAGTFSKMLVPGLRMGYLVAEGPVLRMLARVKRMY 384 Query: 287 DLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPRRDAMLKALEEFMPEGVRWTKPEGGM 346 DL T+ Q ++V+ G H+ YK RRDA+L + +P+ V GG+ Sbjct: 385 DLSTSSVVQRTLERFVDLGSYRAHLTRACRIYKVRRDALLDSAVRHLPDDVTIAPVRGGL 444 Query: 347 FVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAH-RDVKNTMRLNFTYVPEEKIREGIK 405 F W+TLPEG+ ++ +A GV PG FFA + + +R+NFT E + EG++ Sbjct: 445 FAWMTLPEGVGATVLAHEAARHGVTVTPGTPFFAEGLEGERHLRINFTQHDPEILEEGMR 504 Query: 406 RLAETI 411 RLA I Sbjct: 505 RLARAI 510 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: 516 Number of extensions: 36 Number of successful extensions: 4 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: 520 Length adjustment: 33 Effective length of query: 384 Effective length of database: 487 Effective search space: 187008 Effective search space used: 187008 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