Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate 3608082 Dshi_1487 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__Dino:3608082 Length = 693 Score = 166 bits (420), Expect = 2e-45 Identities = 100/308 (32%), Positives = 170/308 (55%), Gaps = 20/308 (6%) Query: 22 KRKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKNK- 80 K+ A +D+S +G+ L ++GESG GK+T +V++GL+ T G ++ D I + Sbjct: 376 KKVVKANEDLSFEAREGETLAIVGESGCGKSTFAKVLMGLETATDGTILLDNREIQDIEI 435 Query: 81 RKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRK-RLINLLELVK 139 + K DVQ++ Q+P+ TL + TV ++ + + + ++ RK R++ LL+LVK Sbjct: 436 QDRDTKTVADVQMVFQNPFDTLNPSMTVGRQIIRALEIFGVGDTEDARKQRMLELLDLVK 495 Query: 140 LTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEI 199 L A F + P QLSGGQKQR+ IAR+ + + RI+VADEPV+ +D S++ + + L EI Sbjct: 496 LPRA--FANRMPRQLSGGQKQRVGIARAFAGDARIVVADEPVSALDVSVQAAVTDLLMEI 553 Query: 200 KNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLI 259 + + T++FI+HD+ I RY +VM+ G +VE +E+ P HPYT L+ Sbjct: 554 QRQNQTTLLFISHDLSIVRYL-----SDRVMVMYLGHVVELGTTDEVFSPPYHPYTEALL 608 Query: 260 KLTPSIDNLYKEINVKINYE-----RVEKGCPYRLRCPFAMDI----CKNEEPKLFK--Y 308 P D ++ + ++ + GCP++ RC + ++ C+ + P K Sbjct: 609 SAVPIADTSIQKERIVLDGDIPSAMNPPPGCPFQTRCRWKSEVPGNLCETQVPPQRKTPT 668 Query: 309 SHEVACFL 316 H++ C L Sbjct: 669 GHQIKCHL 676 Score = 120 bits (301), Expect = 1e-31 Identities = 80/319 (25%), Positives = 172/319 (53%), Gaps = 26/319 (8%) Query: 3 LMELKGVSVIFEDKVGLFKKRKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIV--- 59 ++E++ +S+ F ++ R+ A+ D S ++ G+ + ++GESG GK+T+ ++ Sbjct: 9 ILEIENLSISFFTRL-----REIPAVMDFSCTVMPGEAMGLVGESGCGKSTVALGVMQDL 63 Query: 60 GLQ-KPTSGEVVYDGYNIWKNKRKIFKKYR-KDVQLIPQDPYSTL-PFNKTVEEILVAPI 116 G+ + G + + G ++ + ++ R K++ +I Q+P ++L P + ++++ P+ Sbjct: 64 GVNGRIVGGTIKFKGRDLNTMSPEELRRIRGKEIAMIYQEPMASLNPAMRIGKQLMEVPM 123 Query: 117 LRWEKINKDELRKRLINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIV 176 + E +++D +R ++++ V+L + L +PHQLSGGQ+QR+ IA +L NP +++ Sbjct: 124 IH-EGVSEDVAYQRALDVVTDVRLPDPKRILNSFPHQLSGGQQQRIVIAMALMANPALLI 182 Query: 177 ADEPVTMVDASLRIGILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGR 236 DEP T +D ++ +++ + ++ + +M+FI+H++ + L VM++G Sbjct: 183 LDEPTTALDVTVEAAVVDLVKDLGKKYGTSMLFISHNLGLI-----LETCDRLCVMYSGE 237 Query: 237 IVERADLEEILKDPLHPYTNDLIKL--TPSIDNLYKEI-----NVKINYERVEKGCPYRL 289 VE +E++ + HPYT L + P D + + N + +ER KGC + Sbjct: 238 AVETGSIEDVFDEMQHPYTQALFRSIPLPGADKNARPLVAIPGNFPLPHER-PKGCNFGP 296 Query: 290 RCP-FAMDICKNEEPKLFK 307 C F +C ++ ++ K Sbjct: 297 HCDYFQPGLCDAQDIRMRK 315 Lambda K H 0.321 0.141 0.410 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: 548 Number of extensions: 27 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: 324 Length of database: 693 Length adjustment: 33 Effective length of query: 291 Effective length of database: 660 Effective search space: 192060 Effective search space used: 192060 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: 51 (24.3 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