Align ABC transporter related (characterized, see rationale)
to candidate HSERO_RS05250 HSERO_RS05250 D-ribose transporter ATP binding protein
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__HerbieS:HSERO_RS05250 Length = 520 Score = 370 bits (950), Expect = e-107 Identities = 190/493 (38%), Positives = 318/493 (64%), Gaps = 7/493 (1%) Query: 4 ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63 ++ L+ + K +PGV AL++ L AGEVHAL+GENGAGKSTL+K+++G +D GDIL Sbjct: 22 VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81 Query: 64 LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRR-LGL-IHFKKMYADA 121 G+P P AQ GI ++QE+NL+ +L+ AQN+F+G EPR+ +GL I ++ A Sbjct: 82 DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQA 141 Query: 122 RAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFG 181 A+ + +LD+D S P+ + ++A QQ++ IA+ ++ ++VL++DEPTA+L+ E+ LF Sbjct: 142 AAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201 Query: 182 ILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSL 241 I+ L+A+GV IV+I+H +D++ QI+DR++V+R+G++I E +I M+GR+L Sbjct: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRAL 261 Query: 242 QEQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVC 301 D +++ T V+L + ++ +I+ ++ T+ KG+ +G AGL+G+GR+EV Sbjct: 262 -----DGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVA 316 Query: 302 NAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILAL 361 A+FG D +++G I + G K + P DA++ GI EDRK G+ + ++ NI L+ Sbjct: 317 RAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSS 376 Query: 362 QARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPIL 421 R ++ +E AQ ++ +L I TP ++ LSGGNQQK+++A+WL + + Sbjct: 377 MGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDI 436 Query: 422 LVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVRE 481 L DEPTRGID+GA +EI KL+ L ++G ++++ SSEL E++ S++V+V+ + E Sbjct: 437 LFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGE 496 Query: 482 LSGAELTSQHVMQ 494 L+ A+ T + +MQ Sbjct: 497 LARADATQEKIMQ 509 Lambda K H 0.319 0.136 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: 571 Number of extensions: 31 Number of successful extensions: 7 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: 499 Length of database: 520 Length adjustment: 34 Effective length of query: 465 Effective length of database: 486 Effective search space: 225990 Effective search space used: 225990 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