Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate AZOBR_RS31245 AZOBR_RS31245 ABC transporter ATP-binding protein
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__azobra:AZOBR_RS31245 Length = 518 Score = 333 bits (855), Expect = 7e-96 Identities = 204/503 (40%), Positives = 302/503 (60%), Gaps = 16/503 (3%) Query: 9 ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADR--GTI 66 IL +G++K FPGVKALD+V+ S+R GEI AL+GENGAGKSTL+K L+GVY G I Sbjct: 5 ILEMKGITKTFPGVKALDDVNLSVREGEIHALIGENGAGKSTLMKVLSGVYPQGSFDGEI 64 Query: 67 WLEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRA 126 GQ + + A +++LGI ++QE+ L+P +S+ +NLF+G E G++ RA Sbjct: 65 RFRGQPQAFRGIADSERLGIIIIHQELALVPLLSITENLFLGNEQASRGVIDWDAATLRA 124 Query: 127 TELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFD 186 EL+ G + V QQ+V I +A+ K+LILDEPTASL+ + + L + Sbjct: 125 RELLRLVGLHDPPETLITDIGVGKQQLVEIAKALSKEVKLLILDEPTASLNESDSDALLE 184 Query: 187 LMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFV---GCRETCELPQIELVKMMLG 243 L+ Q + RG++ I ++H L+++ +V+DR+T+LR+G+ V CRE + Q +++ M+G Sbjct: 185 LLLQFKARGIASILISHKLNEIAKVADRVTILRDGTTVETLDCREAV-VSQDRIIRGMVG 243 Query: 244 RELDTHALQRA---GRTLLSDKPVAA-FKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGR 299 R L +R G L K +A + + + +L VR GE+VG+AGL+G+GR Sbjct: 244 RALSDRYPRRTTVPGDVLFEVKGWSADHPAHPGRRVVRDVNLTVRRGEVVGIAGLMGAGR 303 Query: 300 TETAEVIFGIKPADS--GTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRE 357 TE A +FG + G A + G+ ++ + +A G+ + EDRK G++ +R Sbjct: 304 TEFAMSLFGRSYGRNIRGQAFLDGREIDVSTISRAMANGLAYATEDRKHLGLVLDNDIRH 363 Query: 358 NIILA--LQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSR 415 N+ LA + W+ I + + ++AE F R+L IR Q LSGGNQQKV+LS+ Sbjct: 364 NVTLANLRGVAKRWV--IDHEREVQVAEEFRRRLRIRCADVFQETVNLSGGNQQKVVLSK 421 Query: 416 WLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIM 475 WL PQ LILDEPTRGIDVGA EI +I L A+G +++ISSE+ EL+G ADR+ +M Sbjct: 422 WLFADPQVLILDEPTRGIDVGAKYEIYTIINQLVAEGRGVVLISSEMPELLGVADRIYVM 481 Query: 476 RDRKQVAEIPLAELSVPAIMNAI 498 + VAE+P AE S IM AI Sbjct: 482 NAGEMVAEMPAAEASQEKIMGAI 504 Lambda K H 0.321 0.138 0.391 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: 613 Number of extensions: 31 Number of successful extensions: 9 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: 500 Length of database: 518 Length adjustment: 34 Effective length of query: 466 Effective length of database: 484 Effective search space: 225544 Effective search space used: 225544 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