Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate SM_b21344 SM_b21344 sugar uptake ABC transporter ATP-binding protein
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__Smeli:SM_b21344 Length = 497 Score = 422 bits (1085), Expect = e-122 Identities = 225/492 (45%), Positives = 314/492 (63%), Gaps = 1/492 (0%) Query: 9 ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68 +L +G+ K F G+ AL + E+MAL+G+NGAGKSTLIK LTG Y D G + Sbjct: 2 LLSMQGICKSFNGIPALRAASLEVGEAEVMALVGQNGAGKSTLIKILTGAYRRDEGAVVF 61 Query: 69 EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128 G+ +S A +Q GI T+YQE+NL P SVA+N+++ REP+RFGL+ R+ M A Sbjct: 62 AGEGVSFSMPAESQARGIATIYQEINLAPQRSVAENIYLSREPRRFGLIDRRAMRDGAAA 121 Query: 129 LMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLM 188 ++ ++ +DV +P+ FS A +Q+VAI RA+ A+++I+DEPT+SLD +EV +LFD + Sbjct: 122 VLRAFNLEIDVDQPVAGFSAATRQMVAIARAVTQKARLVIMDEPTSSLDEREVGILFDTI 181 Query: 189 RQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELDT 248 R L+ GVS++F+ H L+++Y++ DR+T++R+G V ++P++ LV+ MLG+EL Sbjct: 182 RTLKRGGVSVVFIGHRLEELYRICDRVTIMRDGKTVATAAMADMPKLALVRHMLGKELAA 241 Query: 249 HALQRAGRTLLSDKPV-AAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIF 307 + +PV + +N G + L VR GEI GLAGLLGSGRTETA +IF Sbjct: 242 FEAIAKDADEGAQRPVRLSVRNAGAGVRVRDVSLTVREGEISGLAGLLGSGRTETANLIF 301 Query: 308 GIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQR 367 G G G+ + R P A GIG EDRK DGII S+REN+ LAL + Sbjct: 302 GADRLQRGEIRYNGEARAYRQPADAIADGIGLVAEDRKVDGIIPDMSIRENMTLALLPKL 361 Query: 368 GWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILD 427 + R Q EI ER+I L I+ S +QPI+ LSGGNQQKVLL RWL T P+ LI+D Sbjct: 362 ARAGIVDRARQDEIVERYITALAIKCTSPDQPIKELSGGNQQKVLLGRWLCTDPKLLIVD 421 Query: 428 EPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLA 487 EPTRGID+GA +EI+RL+ L +GL +L+ISSELEEL+ ADRV ++ D VA +P Sbjct: 422 EPTRGIDIGAKSEILRLLRRLADEGLGVLMISSELEELLAAADRVTVLSDGTSVAVLPRK 481 Query: 488 ELSVPAIMNAIA 499 ELS A+ A+A Sbjct: 482 ELSEAALFAAMA 493 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: 614 Number of extensions: 28 Number of successful extensions: 6 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: 497 Length adjustment: 34 Effective length of query: 466 Effective length of database: 463 Effective search space: 215758 Effective search space used: 215758 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