Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate 8502321 DvMF_3029 ABC transporter related (RefSeq)
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__Miya:8502321 Length = 537 Score = 236 bits (602), Expect = 1e-66 Identities = 151/469 (32%), Positives = 247/469 (52%), Gaps = 10/469 (2%) Query: 9 ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68 ++R +G+ K F V+A ++ +R G I ALLGENGAGKSTL+ L G D GTI + Sbjct: 29 VVRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIVV 88 Query: 69 EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128 +G + A + GIG VYQ L+ +M+VA+N+ +G+ P LLR M Sbjct: 89 DGVPTVFASPRDALRAGIGMVYQHFMLVDSMTVAENVLLGQSPDM--LLRPARMRDEVAA 146 Query: 129 LMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLM 188 L YG ++D + S+ +Q V I + + ++VLILDEPTA L +E + LF+ M Sbjct: 147 LAERYGLAVDPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLFEAM 206 Query: 189 RQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELP-QIELVKMMLGRELD 247 ++ D+G +L+F++H L +V V+D I +LR G V ++P Q L M+GR++ Sbjct: 207 WRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRMVGRDV- 265 Query: 248 THALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIF 307 LQ + L V + ++ G ++ L+VR GEIV +AG+ G+G+ E E I Sbjct: 266 --VLQVDAKRLTPVDTVLSVEHLSGAG-LSDVSLQVRRGEIVAIAGVAGNGQKELVEAIC 322 Query: 308 GIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQR 367 G+ ++G I G+P G+ + PEDR+ + +N +L + Q Sbjct: 323 GLARPEAGEVRILGRPWREFFAGPPGRRGLAYIPEDRQGLATCRHLDLVDNFLLTTRNQF 382 Query: 368 GWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILD 427 + R E +R + + ++ P LSGGN QK+++ R +P+ ++ + Sbjct: 383 AKGVFLDRTEATNAVKRVVWEYNVQPGDITAPARALSGGNLQKLVIGREFFRKPEVIVAE 442 Query: 428 EPTRGIDVGAHAEII-RLIETLCADGLALLVISSELEELVGYADRVIIM 475 PT+G+D+ A E+ RL+E G +L+++ +L E + ADR+ +M Sbjct: 443 NPTQGLDISATEEVWGRLLEARSTSG--VLLVTGDLNEALELADRIAVM 489 Score = 80.1 bits (196), Expect = 2e-19 Identities = 65/223 (29%), Positives = 110/223 (49%), Gaps = 10/223 (4%) Query: 268 KNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLR 327 K++GK L++RPG I L G G+G++ ++ G D+GT ++ G P Sbjct: 37 KSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIVVDGVPTVFA 96 Query: 328 SPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQRGWLRPIS-RKEQQEIAERFI 386 SP A GIG + ++ + +V EN++L Q+ LRP R E +AER+ Sbjct: 97 SPRDALRAGIGMVYQHFM---LVDSMTVAENVLLG-QSPDMLLRPARMRDEVAALAERY- 151 Query: 387 RQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIE 446 G+ + + LS G +Q+V + + L + LILDEPT + ++ + Sbjct: 152 ---GLAVDPAAR-VGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLFEAMW 207 Query: 447 TLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLAEL 489 + G AL+ IS +L+E++ AD + I+R + V E A++ Sbjct: 208 RMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADV 250 Score = 59.7 bits (143), Expect = 3e-13 Identities = 47/224 (20%), Positives = 100/224 (44%), Gaps = 7/224 (3%) Query: 25 LDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAISPKNTAHAQQL 84 L +V +RRGEI+A+ G G G+ L++A+ G+ + G + + G+ + Sbjct: 291 LSDVSLQVRRGEIVAIAGVAGNGQKELVEAICGLARPEAGEVRILGRPWREFFAGPPGRR 350 Query: 85 GIGTVYQEVNLLP---NMSVADNLFIGREPK--RFGLLRRKEMEKRATELMASYGFSL-D 138 G+ + ++ L ++ + DN + + + L R E ++ Y D Sbjct: 351 GLAYIPEDRQGLATCRHLDLVDNFLLTTRNQFAKGVFLDRTEATNAVKRVVWEYNVQPGD 410 Query: 139 VREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMRQLRDRGVSL 198 + P S Q + I R +V++ + PT LD E ++ + + R + Sbjct: 411 ITAPARALSGGNLQKLVIGREFFRKPEVIVAENPTQGLDISATEEVWGRLLEARSTS-GV 469 Query: 199 IFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMML 242 + VT L++ +++DRI V+ G F+ + + +++ + +M+ Sbjct: 470 LLVTGDLNEALELADRIAVMYRGRFIDVFDKDDTAKVQAIGLMM 513 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: 627 Number of extensions: 41 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 500 Length of database: 537 Length adjustment: 35 Effective length of query: 465 Effective length of database: 502 Effective search space: 233430 Effective search space used: 233430 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