Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein
Query= ecocyc::YTFR-MONOMER (500 letters) >NCBI__GCF_900167125.1:WP_078716498.1 Length = 514 Score = 210 bits (535), Expect = 8e-59 Identities = 145/472 (30%), Positives = 245/472 (51%), Gaps = 16/472 (3%) Query: 9 ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68 ++ +GL+K F V A D++ ++ G + ALLGENGAGKSTL+ L G Y D GTI L Sbjct: 24 LVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIAL 83 Query: 69 EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128 +G+ + + A + GIG VYQ L+ +M+VA+N+ +G+E F L KEM R E Sbjct: 84 DGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQEGSFF--LNPKEMRNRVQE 141 Query: 129 LMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLM 188 L YG +D ++ S+ +Q V I + + ++VLI DEPTA L +E LF+ + Sbjct: 142 LSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFEAL 201 Query: 189 RQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCEL-PQIELVKMMLGRELD 247 ++ ++G S++F++H L++V V+D I +LR G G E+ + +L M+G+E+ Sbjct: 202 WKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADLACRMVGKEV- 260 Query: 248 THALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIF 307 L+ + V +N G + ++ GE+V + G+ G+G+ E I Sbjct: 261 --LLEVDREAMPHGDAVLQVRNLTGIG-LEDITFDLHQGEVVAVVGVAGNGQKALVEAIC 317 Query: 308 GIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQ--- 364 G++ T I GK + + + PEDR ++ +N++L + Sbjct: 318 GLRKPPVDTMFIMGKRWRDFYAKPSWKNSLAYIPEDRLGLATCRNLNLVDNLLLTTRQGF 377 Query: 365 AQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFL 424 A+ WL +K+ I++ IR LSGGN QK +L+R L P+ + Sbjct: 378 ARGPWL---DKKKAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLARELYRCPRLI 434 Query: 425 ILDEPTRGIDVGAHAEIIRLIETLCADGLA-LLVISSELEELVGYADRVIIM 475 + ++PT+G+D+ A ++ L A +A +L+++ +L E + ADRV ++ Sbjct: 435 VAEQPTQGLDIAATEQVWN--HLLAAREMAGILLVTGDLNEALQLADRVAVI 484 Score = 72.8 bits (177), Expect = 3e-17 Identities = 59/227 (25%), Positives = 104/227 (45%), Gaps = 10/227 (4%) Query: 268 KNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLR 327 K +GK L + PG + L G G+G++ ++ G D+GT + GKP Sbjct: 32 KRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIALDGKPVRFS 91 Query: 328 SPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQRGWLRPIS-RKEQQEIAERFI 386 S A GIG + ++ + +V EN++L Q +L P R QE++ R+ Sbjct: 92 SARDAIEAGIGMVYQHFM---LVESMTVAENVLLG-QEGSFFLNPKEMRNRVQELSVRYG 147 Query: 387 RQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIE 446 + P+ + LS G +Q+V + + L + LI DEPT + + + Sbjct: 148 LDID---PAAR--VSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFEALW 202 Query: 447 TLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLAELSVPA 493 + G +++ IS +LEE++ AD + I+R + E +E++ A Sbjct: 203 KIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKA 249 Score = 60.8 bits (146), Expect = 1e-13 Identities = 53/234 (22%), Positives = 114/234 (48%), Gaps = 27/234 (11%) Query: 25 LDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAI-------SPKN 77 L+++ F L +GE++A++G G G+ L++A+ G+ T+++ G+ S KN Sbjct: 286 LEDITFDLHQGEVVAVVGVAGNGQKALVEAICGLRKPPVDTMFIMGKRWRDFYAKPSWKN 345 Query: 78 TAH---AQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATELMASYG 134 + +LG+ T + +NL+ N+ + R P L +K+ + TEL+ + Sbjct: 346 SLAYIPEDRLGLATC-RNLNLVDNLLLTTRQGFARGP----WLDKKKAARDTTELIKKF- 399 Query: 135 FSLDVREPLNRFSVAMQ------QIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLM 188 D+R P ++A Q Q + R + ++++ ++PT LD E +++ + Sbjct: 400 ---DIR-PGRIAALAWQLSGGNLQKSVLARELYRCPRLIVAEQPTQGLDIAATEQVWNHL 455 Query: 189 RQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMML 242 R+ ++ VT L++ Q++DR+ V+ G F+ + ++ + +M+ Sbjct: 456 LAAREMA-GILLVTGDLNEALQLADRVAVIYRGRFMDVFSVSDKQKVNRIGLMM 508 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: 565 Number of extensions: 36 Number of successful extensions: 7 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: 514 Length adjustment: 34 Effective length of query: 466 Effective length of database: 480 Effective search space: 223680 Effective search space used: 223680 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 Apr 09 2024. 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