Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_007056415.1 BL_RS04330 PLP-dependent aminotransferase family protein
Query= BRENDA::A0A060PQX5 (417 letters) >NCBI__GCF_000007525.1:WP_007056415.1 Length = 554 Score = 275 bits (702), Expect = 3e-78 Identities = 145/374 (38%), Positives = 218/374 (58%), Gaps = 13/374 (3%) Query: 46 VISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQYGTTKGFTPLRLALAEWMRKRYDI 105 +I A G P P P +++ +++ E E +GF LR LAE MR R + Sbjct: 187 IIDFATGSPNPADIPDDLLRKVSIEAFESREFDGQPESPIEGFEELRALLAEHMRAR-GV 245 Query: 106 PISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAPTYLAALQAFKYYEPEFVQIPLDDE 165 ++M+ SGS+Q +DLI R FINPGD V+VE T+ ALQ F+ + + +P+D+ Sbjct: 246 QCGVRNVMVLSGSEQGIDLIVRAFINPGDCVLVEQSTFFPALQTFRSADARIIGVPVDEH 305 Query: 166 GMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGVTMSEKRRKRLLELASEYDFLIVED 225 GMR DLL+ + KL+YT+PTFQNP G T+S +RR L+++A Y LIVED Sbjct: 306 GMRTDLLDGYCARF-----RPKLIYTVPTFQNPTGTTLSPERRSELIDVARRYQCLIVED 360 Query: 226 NPYGELRYSGE------PVKPIKAWDDEGRVMYLGTFSKILAPGFRIGWIAAEPHLIRKL 279 + YG+L Y GE P+ P+K ++ G VMYL TFSK + G R GW+ A+PH+I +L Sbjct: 361 DAYGDLWYGGESSDAHRPI-PLKGMENAGYVMYLSTFSKTVTSGLRTGWVVADPHVINRL 419 Query: 280 EIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPRRDAMLKALEEFMPEGVRW 339 ++ VD T+ SQ I + ++ G + H+ +I+ Y+ RRDA + ALE++ P+ V W Sbjct: 420 AALRRMVDQHTSTSSQRICLELLKEGRIAEHLRGLIKAYRIRRDAAIAALEQYAPDEVYW 479 Query: 340 TKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHRDVKNTMRLNFTYVPEEK 399 T P GG ++WV+LP+G+ + +LE ++GV ++PG F + +RLNF Sbjct: 480 TMPAGGYYIWVSLPDGVRSLDVLESCRSQGVTFMPGSVFDVDEMDDSHIRLNFVRPDAAD 539 Query: 400 IREGIKRLAETIKE 413 I GI+ + ETI + Sbjct: 540 IDTGIRIIGETIAQ 553 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: 520 Number of extensions: 27 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: 554 Length adjustment: 34 Effective length of query: 383 Effective length of database: 520 Effective search space: 199160 Effective search space used: 199160 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 12 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