Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate WP_052665037.1 NITAL_RS04930 ABC transporter ATP-binding protein
Query= uniprot:B2T9V9 (510 letters) >NCBI__GCF_000969705.1:WP_052665037.1 Length = 511 Score = 273 bits (697), Expect = 1e-77 Identities = 174/488 (35%), Positives = 260/488 (53%), Gaps = 10/488 (2%) Query: 14 VVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDT--GEV 71 ++E E+TK F AL DV++ V GE HA+ G NGAGKSTL+++L+G+ T GE+ Sbjct: 4 ILEMREITKTFPGVKALEDVNLTVARGEIHAICGENGAGKSTLMNVLSGVYPAGTYTGEI 63 Query: 72 RFSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDA 131 F G + D+ + ++Q +I LSVAEN+F+ + R GVIDW R A Sbjct: 64 VFDGEPVEHQSINDSEALGIVIIHQELALIPHLSVAENIFLGNEQSRRGVIDWHETNRMA 123 Query: 132 RALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFR 191 LL +D G L V +QL+EIA+ALS + +ILDEPTA L+ + L Sbjct: 124 GELLQRVGLDENPTTPVGQLGVGKQQLIEIAKALSKDVKLLILDEPTAALNDQDSAHLLG 183 Query: 192 RISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQ--LIEAMTG- 248 + +L+ EG+T + ISH L E+ EI A T++RD R I + +S Q +I M G Sbjct: 184 LLRQLRAEGITCIMISHKLNELLEIADATTIIRDGRTIETLDMSDPDSNQRRMIRGMVGR 243 Query: 249 ERGGLAVADAAARG--ALPADTAVALELKELTGADYEGVSFTVKRGEVVGLTGATSSGRT 306 + L A G + + + EG + +V+ GE+VG+ G +GRT Sbjct: 244 DIDSLYPERQATLGEEVFRVEDWTVMHPTQAGRVIVEGANLSVRAGEIVGIAGLMGAGRT 303 Query: 307 SVAEAIAGLRAAK--RGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAEN 364 +A +I G + G + + G + V A+++HGI +DR GL L + + N Sbjct: 304 ELAMSIFGRTYGRDVSGQVYMHGQQVDTHTVDAAISHGIAYATEDRKRYGLNLIEDIRRN 363 Query: 365 ASMTIARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALA 424 S + L G ++ A ++ L I A VV LSGGNQQKVV+++ L Sbjct: 364 ISASALGKLSHNGWVDGNQEIAVAERYRRDLDIRAPSVMSVVGKLSGGNQQKVVLSKWLY 423 Query: 425 TNPNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRG 483 T+P +L+L +PT G+DV +K + ++V+R+ E GKAVLV+S EL + L CDR+ + G Sbjct: 424 TDPELLILDEPTRGIDVGAKFEIYTIVNRLAEAGKAVLVISSELPELLGICDRIYTLSAG 483 Query: 484 RVAAEFPA 491 R+ E PA Sbjct: 484 RITGELPA 491 Score = 45.8 bits (107), Expect = 4e-09 Identities = 30/99 (30%), Positives = 46/99 (46%) Query: 149 GDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQREGVTFLFISH 208 G LS +Q V +++ L +ILDEPT +D ++ ++ L G L IS Sbjct: 406 GKLSGGNQQKVVLSKWLYTDPELLILDEPTRGIDVGAKFEIYTIVNRLAEAGKAVLVISS 465 Query: 209 HLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMT 247 L E+ IC + L R P + +E+L+E MT Sbjct: 466 ELPELLGICDRIYTLSAGRITGELPAAEATQERLMELMT 504 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: 624 Number of extensions: 29 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 510 Length of database: 511 Length adjustment: 35 Effective length of query: 475 Effective length of database: 476 Effective search space: 226100 Effective search space used: 226100 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 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