Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate GFF2673 PS417_13635 D-ribose transporter ATP-binding protein
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__WCS417:GFF2673 Length = 510 Score = 343 bits (880), Expect = 8e-99 Identities = 201/488 (41%), Positives = 298/488 (61%), Gaps = 18/488 (3%) Query: 7 QEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRG-T 65 + +L +G+SK F G++ L V + GEI AL+GENGAGKSTL+K L+G Y AD G Sbjct: 4 EPLLEMQGISKTFNGLRVLKTVGLKVYPGEIHALMGENGAGKSTLMKILSGAYQADPGGE 63 Query: 66 IWLEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKR 125 I + GQ I + A A+ LGI +YQE++L PN+SVA+N+++GRE +R + RK ME Sbjct: 64 IRIAGQLIPTFDPATAKALGIAVIYQELSLCPNLSVAENIYLGRELRRGWTIDRKGMEAG 123 Query: 126 ATELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLF 185 E++ G ++ S+A +Q+V I RA+ AK+L++DEPT L ++E + LF Sbjct: 124 CIEVLQRLGAEFTPATRVSSLSIAERQLVEIARALHAHAKILVMDEPTTPLSSRETDRLF 183 Query: 186 DLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRE 245 L++QLR +G+++I+++H + ++Y +SDR++VLR+G ++G L LVKMM+GR+ Sbjct: 184 ALIKQLRSQGLAIIYISHRMAEIYALSDRVSVLRDGHYIGELTRDALSAEALVKMMVGRD 243 Query: 246 LD-----THALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRT 300 L HA G ++ + +A GK+ FDL GE++G+AGL+G+GRT Sbjct: 244 LSGFYKKEHAAYNPGNVVMRVRDMAD----GKRVRHCSFDLHA--GEVLGIAGLVGAGRT 297 Query: 301 ETAEVIFGIKPADSGTALIKGKPQN-LRSPHQASVLGIGFCPEDRKTDGIIAAASVRENI 359 E A +IF P SGT + GK LR+P A G+ + EDRK G+ SV +NI Sbjct: 298 ELARLIFAADPRTSGTLEVVGKAVTPLRTPADAIRAGVVYLTEDRKAQGLFLDMSVADNI 357 Query: 360 ILAL---QAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRW 416 + A G + + R + + I+ L IR S + LSGGNQQKVLL+R Sbjct: 358 NVCACVPDAHAGGV--LDRDHALQRSNDAIKSLSIRVASGKVNAGALSGGNQQKVLLARL 415 Query: 417 LLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMR 476 L +P LILDEPTRG+D+G+ +EI R+I L G+ ++VISSEL E++G DRV+IMR Sbjct: 416 LEVKPHVLILDEPTRGVDIGSKSEIYRIINQLAQAGIGIVVISSELPEIIGTCDRVLIMR 475 Query: 477 DRKQVAEI 484 + + VAE+ Sbjct: 476 EGQLVAEV 483 Score = 88.2 bits (217), Expect = 6e-22 Identities = 67/217 (30%), Positives = 108/217 (49%), Gaps = 9/217 (4%) Query: 281 LEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTAL-IKGKPQNLRSPHQASVLGIGF 339 L+V PGEI L G G+G++ +++ G AD G + I G+ P A LGI Sbjct: 27 LKVYPGEIHALMGENGAGKSTLMKILSGAYQADPGGEIRIAGQLIPTFDPATAKALGIAV 86 Query: 340 CPEDRKTDGIIAAASVRENIILALQAQRGWLRPISRKEQQEIAERFIRQLGIR-TPSTEQ 398 ++ + SV ENI L + +RGW I RK + +++LG TP+T Sbjct: 87 IYQELS---LCPNLSVAENIYLGRELRRGWT--IDRKGMEAGCIEVLQRLGAEFTPATR- 140 Query: 399 PIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVI 458 + LS +Q V ++R L + L++DEPT + + LI+ L + GLA++ I Sbjct: 141 -VSSLSIAERQLVEIARALHAHAKILVMDEPTTPLSSRETDRLFALIKQLRSQGLAIIYI 199 Query: 459 SSELEELVGYADRVIIMRDRKQVAEIPLAELSVPAIM 495 S + E+ +DRV ++RD + E+ LS A++ Sbjct: 200 SHRMAEIYALSDRVSVLRDGHYIGELTRDALSAEALV 236 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: 606 Number of extensions: 32 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 500 Length of database: 510 Length adjustment: 34 Effective length of query: 466 Effective length of database: 476 Effective search space: 221816 Effective search space used: 221816 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