Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_076477443.1 BW971_RS04965 PLP-dependent aminotransferase family protein
Query= BRENDA::A0A060PQX5 (417 letters) >NCBI__GCF_900156495.1:WP_076477443.1 Length = 389 Score = 266 bits (680), Expect = 8e-76 Identities = 149/394 (37%), Positives = 235/394 (59%), Gaps = 20/394 (5%) Query: 23 SKKALGMKASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQY 82 S+ ++ S +R+LL++ E DV+S+AGGLPA + P + IAE V+ + A ALQY Sbjct: 9 SRALSSIRGSAIRDLLRVTERPDVLSMAGGLPATDLIPSDRIAEAASRVISE--ASALQY 66 Query: 83 GTTKGFTPLRLALAEWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAPT 142 + G PLR +A+ + ++IT GSQQAL L + ++PGD V+V+ P Sbjct: 67 TVSAGVRPLREVVADRDGTHPE------RVLITHGSQQALFLSAQALLDPGDTVIVDDPV 120 Query: 143 YLAALQAFKYYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGVT 202 Y+ ALQ F+ E V +P+ EG VD LE L + G + ++V+T+ F NPAGVT Sbjct: 121 YVGALQVFQSVRAEIVALPITAEGTDVDRLERLLSD----GVRPRIVHTVSNFHNPAGVT 176 Query: 203 MSEKRRKRLLELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVMYLGTFSKILAP 262 S + R+RL ELA+++ F I+ED+PYG+LR++G + PI RV+ LG+ SKILAP Sbjct: 177 ASARTRRRLAELAADHGFWIIEDDPYGQLRFAGRSMDPIPG----DRVIRLGSASKILAP 232 Query: 263 GFRIGWIAAEPHLIRKLEIAKQSVDLCTNPFSQVIAWKYV-EGGHLDNHIPNIIEFYKPR 321 R+GW+ A P ++ +E+ +Q DLC + F+Q++ + + + H+ ++ Y R Sbjct: 233 ALRVGWLQASPDVVELVELLRQGADLCGSTFAQLMTADLLGDSDFMTAHVSDLRREYARR 292 Query: 322 RDAMLKALEEFMPE--GVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFF 379 A+ AL + GV + +PEGGMF W+ LP G+DT ++L+ AV GVA+VPG AF Sbjct: 293 AAALTGALRTDLGAVCGVEFIEPEGGMFCWLRLP-GLDTAILLDHAVRAGVAFVPGAAFA 351 Query: 380 AHRDVKNTMRLNFTYVPEEKIREGIKRLAETIKE 413 + + +RL+F + +++ E ++RLA + + Sbjct: 352 VDAGLGDRLRLSFATLSPDQLTEAVRRLATAVHD 385 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: 336 Number of extensions: 17 Number of successful extensions: 7 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: 389 Length adjustment: 31 Effective length of query: 386 Effective length of database: 358 Effective search space: 138188 Effective search space used: 138188 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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