Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__Putida:PP_2455 Length = 524 Score = 253 bits (647), Expect = 9e-72 Identities = 171/506 (33%), Positives = 266/506 (52%), Gaps = 22/506 (4%) Query: 10 SSVPVV--EALEVTKRFGSTAA---LNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLR 64 S++P + E + G T A L +VS+ + GE AL G NGAGKSTL +++GL Sbjct: 6 SAMPALANEVVLAASGLGKTYAQPVLGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLE 65 Query: 65 KPDTGEVRFSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDW 124 P TG + + G A + +A R V V Q ++ L+VAENLF++ P R G I Sbjct: 66 VPTTGHMTYRGQAYAPGSRGEAERLGVRMVMQELNLLPTLTVAENLFLDNLPSRFGWISH 125 Query: 125 QAMRRDARALLDHWKID-VREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDG 183 + +R+ A A + +D + D G+L + +Q+VEIAR L +ILDEPTA L Sbjct: 126 KRLRQLATAAMARVGLDAIDPDTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTA 185 Query: 184 DEIKRLFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLI 243 E+ LF +I L+ GV ++ISH L+E+ + Q + VLRD + + P+ +L+ Sbjct: 186 REVALLFTQIERLRARGVAIVYISHRLEELQRVAQRIVVLRDGKLVCDEPIQRYSSAELV 245 Query: 244 EAMTGERGGLAVADAAARGALPADTAVALELKELTGAD-YEGVSFTVKRGEVVGLTGATS 302 M G G + + P L++ +L D VSF V+ GE+ G++G Sbjct: 246 NLMVGRELGEHIDLGRRQLGAPL-----LKVDKLCRGDKVREVSFEVRAGEIFGISGLIG 300 Query: 303 SGRTSVAEAIAGLRAAKRGTISVDGAILPPGDVP-----ASLAHGIGCVPKDRHHEGLVL 357 +GRT + I G A G I++ PP V A++ GI + +DR EGL+L Sbjct: 301 AGRTELLRLIYGADRADSGGIALGQ---PPQAVSIDSPKAAVRAGIALITEDRKGEGLLL 357 Query: 358 TQSVAENASMTIARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKV 417 TQS++ N ++ + + G+ + A ++ I A+ I + G + VV LSGGNQQKV Sbjct: 358 TQSISANIALGNLGAVSRAGVLDSEAEKALAERQIQAMRIRSAGAQQVVGELSGGNQQKV 417 Query: 418 VMARALATNPNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDDLR-TCDR 476 V+ R L + VL+ +PT G+DV +K + ++ + +GKA++VVS +L +L CDR Sbjct: 418 VIGRWLERDCQVLLFDEPTRGIDVGAKFDIYGLLAELARQGKALVVVSSDLRELMLICDR 477 Query: 477 VLVMFRGRVAAEFPAG-WQDHDLIAS 501 + V+ GR+ F W L+A+ Sbjct: 478 IAVLSAGRLIDTFARDHWSQDQLLAA 503 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: 581 Number of extensions: 28 Number of successful extensions: 9 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 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