Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__Cola:Echvi_1282 Length = 502 Score = 272 bits (695), Expect = 2e-77 Identities = 167/479 (34%), Positives = 263/479 (54%), Gaps = 11/479 (2%) Query: 20 VTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAP 79 +TK F AL+DVS+ + G A++G NGAGKSTL+ IL+G+ G + ++G Sbjct: 7 ITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYYNGDPVK 66 Query: 80 SIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRG-GVIDWQAMRRDARALLDHW 138 RDA + + ++Q +I LS+ EN+F+ R+P G++D M ++A LL Sbjct: 67 FQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREPETPMGLLDVAKMHKEAAQLLHRL 126 Query: 139 KIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQR 198 K++V + L V +QLVEIA+ALS ++ II+DEPT+ + E++ LF I L+ Sbjct: 127 KLNVDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILFGIIRALRA 186 Query: 199 EGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGERGGLAVADA 258 EG +ISH L E++ I VLRD + I S + + E LI+ M G V + Sbjct: 187 EGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMVGRE---IVIER 243 Query: 259 AARGALPADTAVA---LELKELTGAD---YEGVSFTVKRGEVVGLTGATSSGRTSVAEAI 312 + G +T ++ L +K AD + ++F + +GEV+G+ G +GRT + EA+ Sbjct: 244 SCSGRQFDETVLSVKHLTVKHPKIADKFLLQDINFELGKGEVLGIFGLMGAGRTELMEAL 303 Query: 313 AGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIARV 372 G+ + I++ G + ++ G+ VP+DR +GLVL + N+S+T+ Sbjct: 304 FGVLPHQGAEITLAGKVHEFQKPQEAMDAGLALVPEDRKQDGLVLCMDLCTNSSLTVVDS 363 Query: 373 LGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVLVL 432 + G+ K+ QK + L I A +V LSGGNQQKVV+A+ LAT P VL+L Sbjct: 364 ILSGGLLDDKKEKGLAQKYMGELKIKASSHRQLVEKLSGGNQQKVVLAKWLATRPKVLML 423 Query: 433 IDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRGRVAAEFP 490 +PT G+D+ +K + ++ ++ EG ++VVS EL + L DRVLVM GR+ A P Sbjct: 424 DEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRVLVMAEGRLTANIP 482 Score = 65.5 bits (158), Expect = 4e-15 Identities = 52/220 (23%), Positives = 99/220 (45%), Gaps = 6/220 (2%) Query: 30 LNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAPSIADRDAWRE 89 L D++ + GE + G GAG++ L+ L G+ E+ +G ++A Sbjct: 273 LQDINFELGKGEVLGIFGLMGAGRTELMEALFGVLPHQGAEITLAGKVHEFQKPQEAMDA 332 Query: 90 RVACVYQHS-----TIIRDLSVAENLFINRQPLRGGVIDWQAMRRDARALLDHWKIDVRE 144 +A V + + DL +L + L GG++D + + A+ + KI Sbjct: 333 GLALVPEDRKQDGLVLCMDLCTNSSLTVVDSILSGGLLDDKKEKGLAQKYMGELKIKASS 392 Query: 145 DARAGD-LSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQREGVTF 203 + + LS +Q V +A+ L+ + ++LDEPT +D + +++ I +L EG+ Sbjct: 393 HRQLVEKLSGGNQQKVVLAKWLATRPKVLMLDEPTRGIDINAKNEIYKLIRQLANEGLGL 452 Query: 204 LFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLI 243 + +S L E+ + V V+ + R + P+ A E I Sbjct: 453 IVVSSELPEILAVSDRVLVMAEGRLTANIPIDAQTSEDEI 492 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: 508 Number of extensions: 31 Number of successful extensions: 7 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: 502 Length adjustment: 34 Effective length of query: 476 Effective length of database: 468 Effective search space: 222768 Effective search space used: 222768 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