Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate 16017 b1900 fused L-arabinose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__Keio:16017 Length = 504 Score = 335 bits (860), Expect = 2e-96 Identities = 195/512 (38%), Positives = 303/512 (59%), Gaps = 27/512 (5%) Query: 5 QHQEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRG 64 Q L G+ K FPGVKAL ++ F G++ AL+GENGAGKSTL+K L+G Y G Sbjct: 3 QSTPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTG 62 Query: 65 TIWLEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEK 124 ++ + GQ +S +T A G+ +YQE++L+P M+VA+N+++G+ P + G++ R + Sbjct: 63 SVVINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNY 122 Query: 125 RATELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELL 184 A + G +D PL S+ Q+V I +A+ +AK++ DEPT+SL +E++ L Sbjct: 123 EAGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNL 182 Query: 185 FDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIE---LVKMM 241 F ++R+LR G +++V+H +++++ +SD ITV ++G +V + ++ Q++ LV+ M Sbjct: 183 FRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYV--KTFTDMQQVDHDALVQAM 240 Query: 242 LGREL-DTHALQ--RAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSG 298 +GR++ D + Q G L V A G P L VR GEIVGL GL+G+G Sbjct: 241 VGRDIGDIYGWQPRSYGEERLRLDAVKA------PGVRTPISLAVRSGEIVGLFGLVGAG 294 Query: 299 RTETAEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVREN 358 R+E + +FG +G I +P ++R P A G+ CPEDRK +GII SVR+N Sbjct: 295 RSELMKGMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDN 354 Query: 359 IILALQAQR---GWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSR 415 I ++ + + G + I+ ++ A+ IR L I+TP EQ I LSGGNQQK +L R Sbjct: 355 INISARRKHVLGGCV--INNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGR 412 Query: 416 WLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIM 475 WL + ++LDEPTRGIDVGA EI +I L A G+A+L SS+L E++G ADR+++M Sbjct: 413 WLSEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVM 472 Query: 476 RD--------RKQVAEIPLAELSVPAIMNAIA 499 R+ +Q E L++P + A+A Sbjct: 473 REGEIAGELLHEQADERQALSLAMPKVSQAVA 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: 565 Number of extensions: 29 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: 500 Length of database: 504 Length adjustment: 34 Effective length of query: 466 Effective length of database: 470 Effective search space: 219020 Effective search space used: 219020 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