Align deoxynucleoside transporter, ATPase component (characterized)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__WCS417:GFF2332 Length = 517 Score = 327 bits (838), Expect = 6e-94 Identities = 186/508 (36%), Positives = 291/508 (57%), Gaps = 15/508 (2%) Query: 3 QQEVSSAPLSQP-------FLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKS 55 Q VS P QP LE+V + K F GV AL V L + G + L+GENG GKS Sbjct: 4 QATVSQPPSLQPQTLEEPYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKS 63 Query: 56 TLIKIISGAQPPDEGQLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTS 115 TL+KII+G PD G++ + G P + L A AGI ++Q+L+L+P+MS+AEN+ + Sbjct: 64 TLMKIIAGIYQPDAGEIRLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGR 123 Query: 116 ELATHEGRLARTFDRRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIA 175 E + R + A L + + + E Q + L +A RQ+V IA+A++ Sbjct: 124 EQLNS----LHMVNHREMHRCTAELLARLRINLDPEEQ---VGNLSIAERQMVEIAKAVS 176 Query: 176 SEAKFVIMDEPTTSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDG 235 ++ +IMDEPT+++T+KEV +L +++A+L++QG +++++HK++E +AI EV V RDG Sbjct: 177 YDSDILIMDEPTSAITEKEVAHLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDG 236 Query: 236 QKMAQGPIAEFTKAQISELMTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLH 295 + + +M GR LS D++L VR T G F DVSF LH Sbjct: 237 HYIGLQRADSMNSDSLISMMVGRELSQLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLH 296 Query: 296 GGEILGVTGLLDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDR 355 GEILG+ GL+ SGR +A + G+ P+ SG + LDG+ + + P A + EDR Sbjct: 297 AGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDR 356 Query: 356 LNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSL 415 GLF + +N+ A++ G I + +AL E K+L++ TP +++ + +L Sbjct: 357 KLSGLFPCLSVLENMEMAVLPHYTGN-GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTL 415 Query: 416 SGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLP 475 SGGNQQ+ L+ RWL +PR+LIL PT G+DVG+K IYR++ L+ G+ +I+IS +LP Sbjct: 416 SGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELP 475 Query: 476 ELLQNCDRILMMKKGHVSAEYRADELSE 503 E+L DR+++M +G + E ++ Sbjct: 476 EVLGMSDRVMVMHEGELMGTLDRSEATQ 503 Score = 70.5 bits (171), Expect = 1e-16 Identities = 56/242 (23%), Positives = 110/242 (45%), Gaps = 10/242 (4%) Query: 267 ESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNELARALAGVAPAQSG 326 E + +IV +GF +DV ++ G +L + G +G++ L + +AG+ +G Sbjct: 19 EEPYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAG 78 Query: 327 DVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMISSLRDRFGQID 386 ++ L G+ I TP A++ I + ++ LN L I +N+ R++ + Sbjct: 79 EIRLRGKPIVFETPLAAQKAGIAMIHQE-LN--LMPHMSIAENIWIG-----REQLNSLH 130 Query: 387 RTRAQALAEQTVKELQIATPGVD--KPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVG 444 + + T + L +D + V +LS +Q V I + ++ D +LI+ PT Sbjct: 131 MVNHREMHRCTAELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSA 190 Query: 445 VDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSAEYRADELSEA 504 + ++ I+ L +G GI+ I+ + E+ D + + + GH RAD ++ Sbjct: 191 ITEKEVAHLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSD 250 Query: 505 DL 506 L Sbjct: 251 SL 252 Score = 65.9 bits (159), Expect = 3e-15 Identities = 53/229 (23%), Positives = 105/229 (45%), Gaps = 8/229 (3%) Query: 32 RGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEGVPHARLSALEALAAG 91 + VS G+I + G G G++ + + I G P GQ+ ++G A+ G Sbjct: 289 KDVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKG 348 Query: 92 IETVYQDLSL---LPNMSVAENVALTSELATHEGRLARTFDRRVLAATAARALEAVGLPG 148 + +D L P +SV EN+ + + L + G ++ L A + + + Sbjct: 349 FALLTEDRKLSGLFPCLSVLENMEM-AVLPHYTGN--GFIQQKALRALCEDMCKKLRVKT 405 Query: 149 NSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEVDNLIAVLANLRAQ 208 S Q I+ L +Q +AR + + + +I+DEPT + + ++A L ++ Sbjct: 406 PSLEQC--IDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASE 463 Query: 209 GVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELMTG 257 G+ V+ +S +L E + V+V+ +G+ M +E T+ ++ +L +G Sbjct: 464 GMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASG 512 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: 562 Number of extensions: 32 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: 517 Length adjustment: 35 Effective length of query: 480 Effective length of database: 482 Effective search space: 231360 Effective search space used: 231360 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 Apr 09 2024. 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