Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate BPHYT_RS20740 BPHYT_RS20740 D-ribose transporter ATP binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__BFirm:BPHYT_RS20740 Length = 503 Score = 407 bits (1045), Expect = e-118 Identities = 241/506 (47%), Positives = 327/506 (64%), Gaps = 16/506 (3%) Query: 12 PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71 PL++++ + K FPGVRAL +V+ AGEVHALMGENGAGKSTLMKIL+G YT D G E Sbjct: 3 PLISVKRLSKRFPGVRALHEVQFELVAGEVHALMGENGAGKSTLMKILAGVYTRDTG-EI 61 Query: 72 HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR-GLVARGDMVRA 130 +GQ V P+ A+ +GV +I+QEL L +L++A+N+++GR + R GL D + A Sbjct: 62 LYEGQPVDFQSPREAQAVGVGIIHQELQLMNHLTIAQNMFIGREPRGRLGLFLDEDKLNA 121 Query: 131 CA-PTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRL 189 A LAR+ P A V+SL++A++Q+VEIA+A+ F++R+L+MDEPT+ L+ E L Sbjct: 122 QAHDILARMHVTLDPRALVSSLTVARQQMVEIAKALSFDSRVLIMDEPTSALNDAEIAEL 181 Query: 190 FALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGR 249 F +IR L+ G+ I+YISH+M E+ ++ADRVTVLRDG +V T+ + A++ MMVGR Sbjct: 182 FRIIRDLKKRGVGIIYISHKMDELKQIADRVTVLRDGEYVATVAVKDTTVQAIIGMMVGR 241 Query: 250 DLSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARL 309 L+ H A + EV L V + G V+ SF LR GE+LG AGL+GAGRTE+AR Sbjct: 242 TLTDAAPSQH-IANQGEVALEVTRLNAGPLVRDVSFALRKGEILGFAGLMGAGRTEVARA 300 Query: 310 VFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHEN 369 VFGAD GE+ + V P A+ GI YL+EDRK GL SV N Sbjct: 301 VFGADPIESGEIVVKG-------VKATIRNPSDAVARGIGYLSEDRKRFGLATGMSVESN 353 Query: 370 INLIVAARDALGLGR-LNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRL 428 I ++ R L L L RT R+ I+ L IR A V LSGGNQQK+++++ Sbjct: 354 I-VMSNLRKFLSLNFFLRRTQIRKTAAHFINLLAIRTPSATQEVRLLSGGNQQKIVIAKW 412 Query: 429 LEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMR 488 LE VL DEPTRG+D+GAKSEIY+L+ +LA G AI+MISSELPE++ + DR++VM Sbjct: 413 LERDCDVLFFDEPTRGIDVGAKSEIYKLLRSLADQGKAIVMISSELPEILRMSDRIVVMC 472 Query: 489 EGTLAGEVRPAGSAAETQERIIALAT 514 EG + GE+ AG+ TQERI+ LAT Sbjct: 473 EGRITGELAAAGA---TQERIMQLAT 495 Score = 79.7 bits (195), Expect = 2e-19 Identities = 63/231 (27%), Positives = 105/231 (45%), Gaps = 12/231 (5%) Query: 29 LRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADP--GGECHIDGQRVQIDGPQSA 86 +R V GE+ G GAG++ + + + GA DP GE + G + I P A Sbjct: 271 VRDVSFALRKGEILGFAGLMGAGRTEVARAVFGA---DPIESGEIVVKGVKATIRNPSDA 327 Query: 87 RDLGVAVIYQE---LSLAPNLSVAENIYLG--RALQRRGLVARGDMVRACAPTLARLGAD 141 G+ + ++ LA +SV NI + R R +R A L A Sbjct: 328 VARGIGYLSEDRKRFGLATGMSVESNIVMSNLRKFLSLNFFLRRTQIRKTAAHFINLLAI 387 Query: 142 FSPAAN--VASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLRGE 199 +P+A V LS +Q + IA+ + + +L DEPT + ++ L+R L + Sbjct: 388 RTPSATQEVRLLSGGNQQKIVIAKWLERDCDVLFFDEPTRGIDVGAKSEIYKLLRSLADQ 447 Query: 200 GMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRD 250 G AI+ IS + EI ++DR+ V+ +G G L A +Q ++++ R+ Sbjct: 448 GKAIVMISSELPEILRMSDRIVVMCEGRITGELAAAGATQERIMQLATQRE 498 Lambda K H 0.320 0.136 0.382 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: 583 Number of extensions: 32 Number of successful extensions: 9 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: 540 Length of database: 503 Length adjustment: 35 Effective length of query: 505 Effective length of database: 468 Effective search space: 236340 Effective search space used: 236340 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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