Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate 8502321 DvMF_3029 ABC transporter related (RefSeq)
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__Miya:8502321 Length = 537 Score = 219 bits (557), Expect = 3e-61 Identities = 156/503 (31%), Positives = 241/503 (47%), Gaps = 27/503 (5%) Query: 13 PVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVR 72 PVV + K FG A +D+++ + PG AL+G NGAGKSTL+SIL G + D G + Sbjct: 28 PVVRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIV 87 Query: 73 FSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDAR 132 G + RDA R + VYQH ++ ++VAEN+ + + P ++ MR + Sbjct: 88 VDGVPTVFASPRDALRAGIGMVYQHFMLVDSMTVAENVLLGQSP--DMLLRPARMRDEVA 145 Query: 133 ALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRR 192 AL + + + V AR G LS+ RQ VEI + L +R +ILDEPTA L E +LF Sbjct: 146 ALAERYGLAVDPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLFEA 205 Query: 193 ISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQ-LIEAMTGERG 251 + + +G +FISH LQEV + + +LR + + +P + L M G Sbjct: 206 MWRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRMVGRD- 264 Query: 252 GLAVADAAARGALPADTAVALELKELTGADYEGVSFTVKRGEVVGLTGATSSGRTSVAEA 311 V A+ P DT +++E L+GA VS V+RGE+V + G +G+ + EA Sbjct: 265 --VVLQVDAKRLTPVDTVLSVE--HLSGAGLSDVSLQVRRGEIVAIAGVAGNGQKELVEA 320 Query: 312 IAGLRAAKRGTISVDGA------ILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENA 365 I GL + G + + G PPG G+ +P+DR + +N Sbjct: 321 ICGLARPEAGEVRILGRPWREFFAGPPG------RRGLAYIPEDRQGLATCRHLDLVDNF 374 Query: 366 SMTIARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALAT 425 +T K + ++++ + LSGGN QK+V+ R Sbjct: 375 LLTTRNQFAKGVFLDRTEATNAVKRVVWEYNVQPGDITAPARALSGGNLQKLVIGREFFR 434 Query: 426 NPNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRGR 484 P V+V +PT G+D+ + E + + R VL+V+G+L++ L DR+ VM+RGR Sbjct: 435 KPEVIVAENPTQGLDISATEEVWGRLLEARST-SGVLLVTGDLNEALELADRIAVMYRGR 493 Query: 485 VAAEFPAGWQDHDLIASVEGVSL 507 F D D A V+ + L Sbjct: 494 FIDVF-----DKDDTAKVQAIGL 511 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: 692 Number of extensions: 38 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: 537 Length adjustment: 35 Effective length of query: 475 Effective length of database: 502 Effective search space: 238450 Effective search space used: 238450 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 Sep 17 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