Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate WP_085121058.1 B9O00_RS01465 ABC transporter permease
Query= SwissProt::P39328 (341 letters) >NCBI__GCF_900177295.1:WP_085121058.1 Length = 335 Score = 150 bits (378), Expect = 6e-41 Identities = 101/301 (33%), Positives = 165/301 (54%), Gaps = 12/301 (3%) Query: 24 QLVALLLVL-LVDSLVAPHFWQVVLQDGRLFGSPIDILNRAAPVALLAIGMTLVIATGGI 82 +++ L LV+ V SL++P+F L + +F +IL+++ + +L+IGMT VI TGGI Sbjct: 35 RMLGLALVIGAVLSLLSPYF----LTESNIF----NILDQSVVIGILSIGMTFVILTGGI 86 Query: 83 DLSVGAVMAIAGATTAAMTVAGFSLPIVLLSALGTGILAGLWNGILVAILKIQPFVATLI 142 DLSVG+V ++G + + + +P+ +L + TG GL +GIL+ ++ FV TL Sbjct: 87 DLSVGSVAGLSGIVLG-LALKDYPIPVAILLGVLTGAGVGLVSGILIGYFRLAAFVVTLG 145 Query: 143 LMVAGRGVAQLITAGQIVTFNSPDLSWFGSGSLLFLPTPVIIAVLTLILFWLLTRKTALG 202 +M GR +A + + ++ DLS + +PT V+ +L W T G Sbjct: 146 MMAIGRSLAYIFSGQTAISGFPSDLSSIVYTDVFGIPTNVLFLGFAYLLAWGYLTYTKGG 205 Query: 203 MFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGIIVAADIRGADANNAGLWLEL 262 I A+G N AA+ AG+ +L YV+SG AA+A A I D G +EL Sbjct: 206 RTIYAIGSNKEAARAAGLGVLFYSILPYVVSGALAAVAITFSVAQILSVDP-LTGNGMEL 264 Query: 263 DAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLSGFPP-EMNQVVKAVVVLCVL 321 DAI AVVIGG SL GGR +++ +++G LI+ + G+ L G P + +++++ +L Sbjct: 265 DAIAAVVIGGASLYGGRGSIVGTLIGVLIMVMIRNGLNLLGVSPFWQGSAIGSIIIMALL 324 Query: 322 I 322 + Sbjct: 325 V 325 Lambda K H 0.327 0.142 0.416 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: 294 Number of extensions: 27 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 341 Length of database: 335 Length adjustment: 28 Effective length of query: 313 Effective length of database: 307 Effective search space: 96091 Effective search space used: 96091 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 49 (23.5 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