Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate Ac3H11_2881 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2881 Length = 496 Score = 272 bits (696), Expect = 2e-77 Identities = 175/475 (36%), Positives = 255/475 (53%), Gaps = 9/475 (1%) Query: 15 VEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFS 74 VE VTK FG L+ V + PG + L+G NGAGKSTL+ IL G P TGEV Sbjct: 5 VEFRNVTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGEVVVD 64 Query: 75 GAA-APSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDARA 133 GA AP R A + + ++Q + DL++A+N+F+ + RG +D +AMR R Sbjct: 65 GAVRAPGGGSRAAEAQGIVLIHQEFNLADDLTIAQNIFLGHEIKRGLFLDDKAMREKTRE 124 Query: 134 LLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRI 193 L + + D R L V +QLVEIARAL+ AR +I+DEPTA L E +RLF + Sbjct: 125 ALAKVGLPLDPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETERLFALM 184 Query: 194 SELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGERGGL 253 + L+ GVT ++ISH L EV V V+RD + +++ R Q+ M G Sbjct: 185 AGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREATASVTRRQMANLMVGRE--- 241 Query: 254 AVADA-AARGALPADTAVALELKELTGADY-EGVSFTVKRGEVVGLTGATSSGRTSVAEA 311 +AD + P D A A+ ++ LT + EGV F V+RGE++G G +GRT + E Sbjct: 242 -LADLFPPKLPAPQDGAPAITVRGLTVPGWAEGVDFEVRRGEILGFAGLVGAGRTELFEG 300 Query: 312 IAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIAR 371 + GLR GT+ + G + + HG+ + +DR +GL + + N ++ Sbjct: 301 LLGLRPRTAGTVEIAGQPVQLKSPRDAARHGLTYLSEDRKGKGLHVHFGLRPNLTLMALE 360 Query: 372 VLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVLV 431 K + PA + A ++ + GI E S LSGGNQQK+ +A+ L P+V+V Sbjct: 361 RYAKPWL-DPAAEQAALREAVQEFGIRTGSLEVRASSLSGGNQQKLALAKVLHPGPSVVV 419 Query: 432 LIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDDL-RTCDRVLVMFRGRV 485 L +PT GVDV +K + +V R+ E+G AV+V+S EL +L C RV VM GR+ Sbjct: 420 LDEPTRGVDVGAKREIYHLVQRLAEQGLAVIVISSELMELIGLCHRVAVMRAGRL 474 Score = 65.5 bits (158), Expect = 4e-15 Identities = 63/232 (27%), Positives = 96/232 (41%), Gaps = 23/232 (9%) Query: 33 VSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAPSIADRDAWRERVA 92 V V GE G GAG++ L L GLR G V +G + RDA R + Sbjct: 274 VDFEVRRGEILGFAGLVGAGRTELFEGLLGLRPRTAGTVEIAGQPVQLKSPRDAARHGLT 333 Query: 93 CVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDARALLDHW--KIDVRE------ 144 + + + L V L N + A+ R A+ LD + +RE Sbjct: 334 YLSEDRKG-KGLHVHFGLRPN--------LTLMALERYAKPWLDPAAEQAALREAVQEFG 384 Query: 145 ------DARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQR 198 + RA LS +Q + +A+ L G ++LDEPT +D + ++ + L Sbjct: 385 IRTGSLEVRASSLSGGNQQKLALAKVLHPGPSVVVLDEPTRGVDVGAKREIYHLVQRLAE 444 Query: 199 EGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGER 250 +G+ + IS L E+ +C V V+R R + L E+LI TG R Sbjct: 445 QGLAVIVISSELMELIGLCHRVAVMRAGRLQTTLQEPHLTEEELIAHATGTR 496 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: 579 Number of extensions: 31 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: 496 Length adjustment: 34 Effective length of query: 476 Effective length of database: 462 Effective search space: 219912 Effective search space used: 219912 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