Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate AO356_01275 AO356_01275 GntR family transcriptional regulator
Query= BRENDA::A0A060PQX5 (417 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_01275 Length = 475 Score = 199 bits (506), Expect = 1e-55 Identities = 117/382 (30%), Positives = 206/382 (53%), Gaps = 19/382 (4%) Query: 22 FSKKALGMKASEVREL---------LKLVESSDVISLAGGLPAPETFPVEIIAEITKEVL 72 FS+ A+ + E E+ L ++ + P+P FP++ ++ Sbjct: 74 FSEPAISTQVHESTEVDVSELVFSVLDSIKDPATVPFGSAFPSPLLFPLQRLSRSLSSAT 133 Query: 73 EKHAAQALQYGTTKGFTPLRLALA-EWMRKRYDIPISKVDIMITSGSQQALDLIGRVFIN 131 + + + G LR +A +M +P+ ++++T+G+ +AL+L + Sbjct: 134 RDMDPRVVVTDMSPGNPHLRRQIALRYMVGGLMLPME--ELLVTNGALEALNLCLQAVTE 191 Query: 132 PGDIVVVEAPTYLAALQAFKYYEPEFVQIPLDD-EGMRVDLLEEKLQELEKEGKKVKLVY 190 PGD+V +EAP + A LQ + + + V+IP+ EG+ +++L + L E +K + Sbjct: 192 PGDLVAIEAPAFYACLQVLERLKLKAVEIPVHPREGIDLEVLAQTL-----ERHPIKACW 246 Query: 191 TIPTFQNPAGVTMSEKRRKRLLELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRV 250 + +FQNP G TM E+R++ L+EL + ++ED+ Y EL Y + KP KA+D EG V Sbjct: 247 CMTSFQNPMGATMPEERKQALVELLRRHQVPLIEDDVYAELYYGQQAPKPAKAFDTEGLV 306 Query: 251 MYLGTFSKILAPGFRIGWIAAEPHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNH 310 M+ G+F+K LAPG+RIGW+AA + +K+E K LC + +Q Y++ G D H Sbjct: 307 MHCGSFAKSLAPGYRIGWVAAGRY-AQKIERLKLMTSLCASMPAQAAIADYLQHGGYDRH 365 Query: 311 IPNIIEFYKPRRDAMLKALEEFMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGV 370 + + + ++ AML A+ + P R ++P GG F+W+ LPE +D+ + + A+A+G+ Sbjct: 366 LRKLRYALEEQQSAMLSAIARYFPAQTRVSQPAGGYFLWLELPEQMDSLKLFQMALAQGI 425 Query: 371 AYVPGEAFFAHRDVKNTMRLNF 392 + PG F A R +N +RLN+ Sbjct: 426 SIAPGPIFSATRRFRNCIRLNY 447 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: 463 Number of extensions: 18 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: 417 Length of database: 475 Length adjustment: 32 Effective length of query: 385 Effective length of database: 443 Effective search space: 170555 Effective search space used: 170555 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