Align deoxynucleoside transporter, ATPase component (characterized)
to candidate 3609577 Dshi_2961 ABC transporter related (RefSeq)
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__Dino:3609577 Length = 511 Score = 254 bits (648), Expect = 7e-72 Identities = 169/496 (34%), Positives = 263/496 (53%), Gaps = 25/496 (5%) Query: 16 LEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIE 75 L V G+ K + GV A VS G+++ LLGENG GKSTL+K+I G PD G + Sbjct: 5 LRVAGLTKAYPGVVANDDVSFEIAEGEVHALLGENGAGKSTLVKMIYGLVRPDSGTMTFG 64 Query: 76 GVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVLAA 135 GVP A A +AG+ V+Q SL ++VAEN+AL E R LAA Sbjct: 65 GVPFAPPEPRAARSAGVAMVFQHFSLFEALTVAENIALGMEDPP---------KMRDLAA 115 Query: 136 TAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEV 195 + +A GLP + S L+ L RQ V I R + E K +IMDEPT+ LT +EV Sbjct: 116 RITQVSQAYGLPLD---PSRLVGTLSAGERQRVEIIRCLLQEPKLLIMDEPTSVLTPQEV 172 Query: 196 DNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELM 255 D L A L LR +G +L++SHKL+E A+ +LR G+ +A E + +++E+M Sbjct: 173 DILFATLRKLRDEGTAILYISHKLEEIRALCDSATILRLGKVVATCDPREKSARELAEMM 232 Query: 256 TGRHLSNERYRESAHAQDIVLDVRGFTRAG------QFSDVSFKLHGGEILGVTGLLDSG 309 G+ L + +A VL++RG ++ D+S ++ GE+LG+ G+ +G Sbjct: 233 VGKTLQQTKSAGNAFGAP-VLELRGLSQPATTPFGTPLRDISLEVRAGEVLGIGGVAGNG 291 Query: 310 RNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYV--PEDRLNEGLFLDKPIR 367 ++EL A++G A+ + L G I+ P A R ++G + PE+RL D + Sbjct: 292 QDELLSAISGERRAEDA-IFLHGTPISKIGP--AARRQLGVLSGPEERLGHAAAPDMSLT 348 Query: 368 DN-VITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIG 426 +N ++T + R G +D + +A AE+ ++ + TPG + ++LSGGN Q+ +IG Sbjct: 349 ENALLTGSVREKLTRNGFLDWAKTRAFAERIIETFDVRTPGPEAAARALSGGNLQKFVIG 408 Query: 427 RWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILM 486 R + P VLI++ PT GVD + I + + L+ G +++IS DL EL++ D Sbjct: 409 REVLQRPEVLIVNQPTWGVDASAAAAIRQALLDLAAGGTAVVVISQDLDELMEISDTFAA 468 Query: 487 MKKGHVSAEYRADELS 502 + G +S + A L+ Sbjct: 469 LNGGRLSGKVPAAGLT 484 Score = 67.8 bits (164), Expect = 9e-16 Identities = 63/245 (25%), Positives = 110/245 (44%), Gaps = 19/245 (7%) Query: 275 VLDVRGFTRAGQF----SDVSFKLHGGEILGVTGLLDSGRNELARALAGVAPAQSGDVLL 330 +L V G T+A DVSF++ GE+ + G +G++ L + + G+ SG + Sbjct: 4 LLRVAGLTKAYPGVVANDDVSFEIAEGEVHALLGENGAGKSTLVKMIYGLVRPDSGTMTF 63 Query: 331 DGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTRA 390 G A P A+ + V + + LF + +N+ G D + Sbjct: 64 GGVPFAPPEPRAARSAGVAMVFQ---HFSLFEALTVAENIA----------LGMEDPPKM 110 Query: 391 QALAEQTVKELQIATPGVD--KPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVG 448 + LA + + Q +D + V +LS G +QRV I R L +P++LI+ PT + Sbjct: 111 RDLAARITQVSQAYGLPLDPSRLVGTLSAGERQRVEIIRCLLQEPKLLIMDEPTSVLTPQ 170 Query: 449 SKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSAEYRADELSEADLYH 508 DI++ +++L G I+ IS L E+ CD +++ G V A E S +L Sbjct: 171 EVDILFATLRKLRDEGTAILYISHKLEEIRALCDSATILRLGKVVATCDPREKSARELAE 230 Query: 509 ALLSE 513 ++ + Sbjct: 231 MMVGK 235 Score = 64.7 bits (156), Expect = 8e-15 Identities = 66/269 (24%), Positives = 110/269 (40%), Gaps = 19/269 (7%) Query: 1 MNQQEVSSAPLSQPFLEVVGVHKRFTGVHA--LRGVSLSFQRGQIYHLLGENGCGKSTLI 58 + Q + + P LE+ G+ + T LR +SL + G++ + G G G+ L+ Sbjct: 237 LQQTKSAGNAFGAPVLELRGLSQPATTPFGTPLRDISLEVRAGEVLGIGGVAGNGQDELL 296 Query: 59 KIISGAQPPDEGQLVIEGVPHARLSALEALAAGIETVYQDL---SLLPNMSVAENVALTS 115 ISG + ++ + + G P +++ G+ + ++ + P+MS+ EN LT Sbjct: 297 SAISGERRAEDA-IFLHGTPISKIGPAARRQLGVLSGPEERLGHAAAPDMSLTENALLTG 355 Query: 116 ---ELATHEGRLARTFDRRVLAATAARALEA--VGLPGNSEFQSTLIEQLPLATRQLVAI 170 E T G L D A A R +E V PG L Q I Sbjct: 356 SVREKLTRNGFL----DWAKTRAFAERIIETFDVRTPG----PEAAARALSGGNLQKFVI 407 Query: 171 ARAIASEAKFVIMDEPTTSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVI 230 R + + +I+++PT + + L +L A G V+ +S LDE I Sbjct: 408 GREVLQRPEVLIVNQPTWGVDASAAAAIRQALLDLAAGGTAVVVISQDLDELMEISDTFA 467 Query: 231 VLRDGQKMAQGPIAEFTKAQISELMTGRH 259 L G+ + P A T QI ++ G H Sbjct: 468 ALNGGRLSGKVPAAGLTVEQIGLMLGGAH 496 Lambda K H 0.319 0.135 0.376 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: 569 Number of extensions: 34 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 515 Length of database: 511 Length adjustment: 35 Effective length of query: 480 Effective length of database: 476 Effective search space: 228480 Effective search space used: 228480 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 (21.7 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