Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate AZOBR_RS31880 AZOBR_RS31880 sugar ABC transporter ATP-binding protein
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__azobra:AZOBR_RS31880 Length = 515 Score = 274 bits (701), Expect = 5e-78 Identities = 174/488 (35%), Positives = 265/488 (54%), Gaps = 7/488 (1%) Query: 9 ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68 +LR G++K F + A D++ +L +GE++ALLGENGAGK+TL+ L G Y AD G+I Sbjct: 7 VLRLSGITKRFGPLVANDSISLTLHKGEVLALLGENGAGKTTLMNILFGHYVADEGSIEA 66 Query: 69 EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128 GQ + P + A GIG V+Q L N+SV DN+ +G E R + + + Sbjct: 67 FGQPLPPGSPRAALAAGIGMVHQHFTLADNLSVLDNIAVGTESLWRPRSDRAAAKAKLLD 126 Query: 129 LMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLM 188 L +G + + SV +Q I +A+ A+VLILDEPTA L QE LFD + Sbjct: 127 LARRFGLEVRPDALVGDLSVGERQRAEILKALYRDARVLILDEPTAVLTPQESASLFDTL 186 Query: 189 RQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGREL-- 246 R+L G++++F++H +++V+ SD + VLR G V R+T E + EL ++M+GR L Sbjct: 187 RRLTADGLAVVFISHKMNEVFAASDTVAVLRGGRLVATRKTAETDREELAELMVGRALKP 246 Query: 247 DTHALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVI 306 T G +L+ V +G+ + DL VR +IVG+AG+ G+G+T AE+I Sbjct: 247 PTPTPLEPGEPVLTLSGVTVASGHGRP-LLDGVDLTVRRRQIVGIAGVSGNGQTALAELI 305 Query: 307 FGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQ 366 G+ DSGT +KG+ P + G+ PEDR G++ A +V EN+I Sbjct: 306 SGLIHPDSGTMTLKGEAIGNAEPAEMVRRGVARIPEDRHAAGLVGAMAVWENLIAERYHD 365 Query: 367 RGWLR--PISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFL 424 + R I R + AE I +R P + + LSGGN QK++L R L P + Sbjct: 366 PAFQRFGLIRRGAARAYAEEVIAAFDVRCPGPDARTQLLSGGNMQKLILGRTLAHGPDLI 425 Query: 425 ILDEPTRGIDVGAHAEII-RLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAE 483 + +PTRG+DVGA + + RL+E A G +LVIS +L+E++ AD + + + Sbjct: 426 LASQPTRGLDVGAVSYVHGRLLEARAA-GAGVLVISEDLDEILALADGITVAYHGRLTPV 484 Query: 484 IPLAELSV 491 +P +SV Sbjct: 485 LPHGRVSV 492 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: 619 Number of extensions: 37 Number of successful extensions: 10 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: 515 Length adjustment: 34 Effective length of query: 466 Effective length of database: 481 Effective search space: 224146 Effective search space used: 224146 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