Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate HSERO_RS22220 HSERO_RS22220 D-ribose transporter ATP-binding protein
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__HerbieS:HSERO_RS22220 Length = 505 Score = 328 bits (840), Expect = 4e-94 Identities = 190/484 (39%), Positives = 281/484 (58%), Gaps = 6/484 (1%) Query: 10 SSVPVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTG 69 S+ PV+ + KRF AL DV V PGE AL+G NGAGKSTLV ILTG+ +PD G Sbjct: 8 STAPVLSLSGIGKRFQGVVALQDVGFTVRPGEVMALLGENGAGKSTLVKILTGIHQPDEG 67 Query: 70 EVRFSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGV--IDWQAM 127 + G + +DA R + V+Q + + +LSVAEN++I RQPL G IDW+ M Sbjct: 68 SIHLGGREVRFASAQDAMRGGITAVHQETVMFEELSVAENIWIGRQPLCGTPRRIDWRRM 127 Query: 128 RRDARALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIK 187 +ARAL ++D+ AR DLSV R VEIARALS A+ +I+DEPTA L EI Sbjct: 128 EDEARALFARLEVDLPVRARVKDLSVAQRHFVEIARALSQQAQVVIMDEPTAALSHHEIG 187 Query: 188 RLFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMT 247 L+R I +L+R G +FISH E+Y + TVLRD R I S ++ + +QL+ M Sbjct: 188 ELYRIIGQLRRAGTAVIFISHKFDEIYAVADRYTVLRDGRFIASGELADITEQQLVALMV 247 Query: 248 GERGGLAVADAAARGALPADTAVALELKELTG-ADYEGVSFTVKRGEVVGLTGATSSGRT 306 G G + AA+ TA LE+K L+ ++++ VSF V+ GE++G G +GR+ Sbjct: 248 GREVGQVFSRAASN--TEDQTAPVLEVKHLSHPSEFDDVSFAVRPGEILGFYGLVGAGRS 305 Query: 307 SVAEAIAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENAS 366 V A+ GL +G + +DG + ++AHG+ VP+DR +G +L+ + +N + Sbjct: 306 EVMHALFGLSPEAQGAVWIDGREVKLCSPAQAIAHGLAYVPEDRQRQGALLSLPIFQNIT 365 Query: 367 MTIARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATN 426 + + +G F ++ +++ + L + A V+ LSGGNQQKVV+A+ LAT Sbjct: 366 LPVLPGIGFFLRRHRRREIDIARRLCEQLELKASHFHQHVAQLSGGNQQKVVLAKWLATQ 425 Query: 427 PNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRGRV 485 P VL+L +PT G+D+ SK A+ + + +G AV++VS EL + + DR++VM +GRV Sbjct: 426 PRVLILDEPTKGIDIGSKAAVHRFIGELVAQGLAVILVSSELPEVMGMSDRIVVMHQGRV 485 Query: 486 AAEF 489 F Sbjct: 486 QQVF 489 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: 592 Number of extensions: 30 Number of successful extensions: 8 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: 505 Length adjustment: 34 Effective length of query: 476 Effective length of database: 471 Effective search space: 224196 Effective search space used: 224196 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