Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate SM_b21376 SM_b21376 sugar uptake ABC transporter ATP-binding protein
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__Smeli:SM_b21376 Length = 503 Score = 367 bits (941), Expect = e-106 Identities = 200/488 (40%), Positives = 299/488 (61%), Gaps = 2/488 (0%) Query: 9 ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68 IL+ ++K F V AL + +RRG + LLGENGAGKSTL+K L GV+ A G I L Sbjct: 9 ILKITDVTKSFGQVAALKGMRLEVRRGRVHTLLGENGAGKSTLMKILAGVHGATSGEIVL 68 Query: 69 EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128 +GQA P N A LG+ V+QE++L N++VA+N+ REP+RFG + K + +A Sbjct: 69 DGQAYRPANPQEAASLGLAIVFQELSLCNNLTVAENILATREPRRFGFINDKALVAKAHR 128 Query: 129 LMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLM 188 ++A +DV E + S+A +Q+V I + + AKV+ILDEPT+SL E E+LF+++ Sbjct: 129 IVADLRLPIDVTEKVGNLSIAQRQLVEIAKGLSHDAKVVILDEPTSSLSDSEAEILFEII 188 Query: 189 RQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELDT 248 +LR RG ++I+++H ++++ ++SD ITV+R+G +V E+ L+ +M+GR +D Sbjct: 189 GRLRQRGAAIIYISHRMEEIMRLSDDITVIRDGEYVSTHARDEVTIETLIALMVGRRMDE 248 Query: 249 HALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFG 308 PV A ++G +VR GEI+G GL+GSGR+E +FG Sbjct: 249 IYPPPVHHVAADRAPVLAVDRLTREGEFQDVSFDVRAGEILGFFGLVGSGRSEVMNALFG 308 Query: 309 IKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQ-R 367 +K A +GT + G+ RSP QA G+GF E+RK +G++ SV NI +A A Sbjct: 309 MKSA-AGTVRLDGEVVRFRSPDQAIARGVGFVTENRKEEGLVLGHSVEWNISMAALADFA 367 Query: 368 GWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILD 427 G L I ++ A + +L I+T S E P LSGGNQQK++L++WLLTRP+ LILD Sbjct: 368 GGLGFIRNGAERAAASEQVGKLSIKTNSLETPAGALSGGNQQKIVLAKWLLTRPKVLILD 427 Query: 428 EPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLA 487 EPTRG+DVGA EI ++I L A+G A+L+ISS+L E++G +DRV++M + A + + Sbjct: 428 EPTRGVDVGAKFEIYKIIRELAAEGTAILLISSDLPEVLGMSDRVVVMHEGAPGATLEGS 487 Query: 488 ELSVPAIM 495 L+ IM Sbjct: 488 ALTPETIM 495 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: 623 Number of extensions: 39 Number of successful extensions: 8 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: 503 Length adjustment: 34 Effective length of query: 466 Effective length of database: 469 Effective search space: 218554 Effective search space used: 218554 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