Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__Cola:Echvi_1282 Length = 502 Score = 358 bits (918), Expect = e-103 Identities = 192/500 (38%), Positives = 312/500 (62%), Gaps = 16/500 (3%) Query: 9 ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68 +L + ++K F GVKALD+V L+ G + A+LGENGAGKSTL+K L+GVY +GTI+ Sbjct: 1 MLTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYY 60 Query: 69 EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKR-FGLLRRKEMEKRAT 127 G + +NT AQ+ GI ++QE+NL+P +S+ +N+F+GREP+ GLL +M K A Sbjct: 61 NGDPVKFQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREPETPMGLLDVAKMHKEAA 120 Query: 128 ELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDL 187 +L+ ++D P+++ V QQ+V I +A+ L ++V+I+DEPT+++ QEVE+LF + Sbjct: 121 QLLHRLKLNVDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILFGI 180 Query: 188 MRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELD 247 +R LR G ++ +++H LD+++ ++DR VLR+G + E + + L++ M+GRE+ Sbjct: 181 IRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMVGREI- 239 Query: 248 THALQRAGRTLLSDKPVAAFKNY-------GKKGTIAPFDLEVRPGEIVGLAGLLGSGRT 300 ++R+ D+ V + K+ K + + E+ GE++G+ GL+G+GRT Sbjct: 240 --VIERSCSGRQFDETVLSVKHLTVKHPKIADKFLLQDINFELGKGEVLGIFGLMGAGRT 297 Query: 301 ETAEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENII 360 E E +FG+ P + GK + P +A G+ PEDRK DG++ + N Sbjct: 298 ELMEALFGVLPHQGAEITLAGKVHEFQKPQEAMDAGLALVPEDRKQDGLVLCMDLCTNSS 357 Query: 361 LAL--QAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLL 418 L + G L + K+++ +A++++ +L I+ S Q +E LSGGNQQKV+L++WL Sbjct: 358 LTVVDSILSGGL--LDDKKEKGLAQKYMGELKIKASSHRQLVEKLSGGNQQKVVLAKWLA 415 Query: 419 TRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDR 478 TRP+ L+LDEPTRGID+ A EI +LI L +GL L+V+SSEL E++ +DRV++M + Sbjct: 416 TRPKVLMLDEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRVLVMAEG 475 Query: 479 KQVAEIPL-AELSVPAIMNA 497 + A IP+ A+ S I+ A Sbjct: 476 RLTANIPIDAQTSEDEILQA 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: 583 Number of extensions: 30 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: 502 Length adjustment: 34 Effective length of query: 466 Effective length of database: 468 Effective search space: 218088 Effective search space used: 218088 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