Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein (TIGR)
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__DvH:206505 Length = 524 Score = 222 bits (565), Expect = 3e-62 Identities = 148/473 (31%), Positives = 234/473 (49%), Gaps = 11/473 (2%) Query: 13 PVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVR 72 PVV + K FG A +D+++ ++PG AL+G NGAGKSTL+SIL+G DTG + Sbjct: 33 PVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIH 92 Query: 73 FSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDAR 132 G A + +DA + + VYQH ++ ++VAEN+ + + G + M R Sbjct: 93 VDGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQS---GAWLSPVHMSRVVA 149 Query: 133 ALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRR 192 L + +D+ AR DLS+ RQ VEI + L +R +ILDEPTA L E ++LF Sbjct: 150 ELAARYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEA 209 Query: 193 ISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPRE-QLIEAMTGERG 251 + + G +FISH +QEV + + +LR + S +P E +L M G Sbjct: 210 LHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANRMVGRE- 268 Query: 252 GLAVADAAARGALPADTAVALELKELTGADYEGVSFTVKRGEVVGLTGATSSGRTSVAEA 311 + + AA P D L + L G +G+SF V++GEV + G +G+ + E Sbjct: 269 --VILEVAAEPLEPGDR--VLHVDGLAGDGLKGLSFEVRKGEVFAIAGVAGNGQRELVEC 324 Query: 312 IAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIAR 371 + GLR G + + G A G+ +P+DR L+ + +N +T Sbjct: 325 VTGLRRPAEGEVELLGIPWRQFFTKAPRQGGLAYIPEDRQGLATCLSLDLVDNFLLTARG 384 Query: 372 VLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVLV 431 + +A + ++ + E LSGGN QK+V+ R P+++V Sbjct: 385 CFTRGPFLDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVGREFYRKPSLIV 444 Query: 432 LIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRG 483 +PT G+D+ + E + + + VR VL+VSG+L++ L DRV VM+RG Sbjct: 445 AENPTQGLDIAATEEVWARLLEVRSHA-GVLLVSGDLNEVLALADRVAVMYRG 496 Lambda K H 0.318 0.134 0.377 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: 652 Number of extensions: 30 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: 510 Length of database: 524 Length adjustment: 35 Effective length of query: 475 Effective length of database: 489 Effective search space: 232275 Effective search space used: 232275 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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