Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_012407473.1 NPUN_RS03530 PLP-dependent aminotransferase family protein
Query= BRENDA::A0A060PQX5 (417 letters) >NCBI__GCF_000020025.1:WP_012407473.1 Length = 399 Score = 249 bits (636), Expect = 1e-70 Identities = 144/380 (37%), Positives = 212/380 (55%), Gaps = 15/380 (3%) Query: 36 ELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQYGTTKGFTPLRLAL 95 EL K+V +S A GL P FP +A + VL + A AL YG P L Sbjct: 29 ELSKIV----TVSFAYGLADPILFPHTDLAAASAVVLAEEAPIALNYG------PPSAQL 78 Query: 96 AEWMRKRYD---IPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAPTYLAALQAFKY 152 E + R I + ++I GS Q L L+ VF+ PGD+V+VE PT+L + F + Sbjct: 79 YEQIILRLQAKGIAADRDRLIIGYGSGQILGLLPDVFVEPGDVVIVEGPTFLGVVTRFVH 138 Query: 153 YEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGVTMSEKRRKRLL 212 + IP+D+ GM VD LE L +L+K+G + + +YTIPTF NP G TM RR++L+ Sbjct: 139 AGARIITIPVDELGMDVDALEVTLNDLKKQGIRPRFIYTIPTFHNPTGATMPLFRRQKLV 198 Query: 213 ELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVMYLGTFSKILAPGFRIGWIAAE 272 LA+EY LIVED+ Y +LR+ GE + + D EG V+Y+ TFSKI+APG R+GW + Sbjct: 199 ALAAEYGVLIVEDDAYSDLRFRGETMPSLATLDQEGWVLYVSTFSKIIAPGIRLGWACGD 258 Query: 273 PHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPRRDAMLKALEEF 332 +I +L + K + PF + +Y G LDNHI +I YK + + +L+A+ + Sbjct: 259 ATIIERLAMFKS--EGTVGPFVSHVVARYCATGKLDNHIQELIACYKHKCNLLLEAIAQE 316 Query: 333 MPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHRDVKNTMRLNF 392 P V +P+GG FVW LP I K +L A G++++PG +A+ + +RL F Sbjct: 317 FPSDVVALRPDGGFFVWCKLPPDISAKALLMAASEHGISFLPGTRCYANGQGDDAIRLAF 376 Query: 393 TYVPEEKIREGIKRLAETIK 412 ++ P +KI EGI L ++ Sbjct: 377 SFQPTQKIVEGIATLGSVLR 396 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: 385 Number of extensions: 19 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: 399 Length adjustment: 31 Effective length of query: 386 Effective length of database: 368 Effective search space: 142048 Effective search space used: 142048 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: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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