Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate 3607108 Dshi_0530 ABC transporter related (RefSeq)
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__Dino:3607108 Length = 498 Score = 308 bits (788), Expect = 4e-88 Identities = 176/507 (34%), Positives = 291/507 (57%), Gaps = 16/507 (3%) Query: 1 MTTDQHQEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYH 60 M++D + ++K + GV ALD+VDF+++ GE + L GENG+GKSTLIK ++GV Sbjct: 1 MSSDHDTAFIDLRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEP 60 Query: 61 ADRGTIWLEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNL-FIGREPKRFGLLRR 119 A GT+ + GQ N + G+ ++Q+ +L PN+SVA+N+ F + R L + Sbjct: 61 ATAGTVQIAGQEHVTLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKF 120 Query: 120 KEMEKRATELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQ 179 + + A + G +D+ + VA +Q+VAICRA+ A+++I+DEPT +L + Sbjct: 121 RAVRDIARAALDRIGVQIDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEK 180 Query: 180 EVELLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVK 239 EV L ++R L++ GV++IFV+H L +V +VS+++ VLRNG V E L Sbjct: 181 EVRRLQGIIRMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTY 240 Query: 240 MMLGR---ELDTHALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLG 296 M GR E+ + +TL+ + GK G+ + ++R GE++G+ GLLG Sbjct: 241 HMTGRDVPEVPPSDVAAGAQTLMQ------VQGLGKAGSFSDISFDLRTGEVLGITGLLG 294 Query: 297 SGRTETAEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVR 356 GRT A+ +FG+ D+G+ L+ G P L P AS+ IG+ PEDR T+G+ + S+ Sbjct: 295 CGRTSVAKALFGLVTPDAGSILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSIL 354 Query: 357 ENII---LALQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLL 413 N+ L G+L ++ A ++R+L ++ P E P++ LSGGNQQ+V L Sbjct: 355 RNVAVGRLDAHTSGGFLDMTGLAKE---ASDWLRRLKVKAPDVEAPVQSLSGGNQQRVAL 411 Query: 414 SRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVI 473 +RWL P+ LIL+ P+ G+DVG+ A+I +I L +G+ ++VIS +L EL+ RV+ Sbjct: 412 ARWLSRAPRVLILNGPSVGVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVL 471 Query: 474 IMRDRKQVAEIPLAELSVPAIMNAIAA 500 +MR+ + + + L+ + + +A+ Sbjct: 472 VMREGRIIDALEGTALTEDDLAHRLAS 498 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: 521 Number of extensions: 24 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: 498 Length adjustment: 34 Effective length of query: 466 Effective length of database: 464 Effective search space: 216224 Effective search space used: 216224 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