Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate AZOBR_RS31205 AZOBR_RS31205 sugar ABC transporter permease
Query= SwissProt::P39328 (341 letters) >FitnessBrowser__azobra:AZOBR_RS31205 Length = 354 Score = 386 bits (992), Expect = e-112 Identities = 201/304 (66%), Positives = 245/304 (80%) Query: 22 MPQLVALLLVLLVDSLVAPHFWQVVLQDGRLFGSPIDILNRAAPVALLAIGMTLVIATGG 81 +PQ AL VLL + L+ P F+ + LQDGRLFGS ID+LNR APVALLAIGMT+VIAT G Sbjct: 12 LPQYGALAAVLLANWLLFPDFFSIRLQDGRLFGSLIDVLNRGAPVALLAIGMTMVIATRG 71 Query: 82 IDLSVGAVMAIAGATTAAMTVAGFSLPIVLLSALGTGILAGLWNGILVAILKIQPFVATL 141 +DLSVGAVMAI+GA A +T AG+ L VL ++L G+L GLWNG+LVA+L+IQP VATL Sbjct: 72 VDLSVGAVMAISGAVAATLTQAGWGLTPVLAASLAAGLLCGLWNGLLVAVLRIQPIVATL 131 Query: 142 ILMVAGRGVAQLITAGQIVTFNSPDLSWFGSGSLLFLPTPVIIAVLTLILFWLLTRKTAL 201 ILMVAGRG+AQL+T GQIVTF SP L++ GSGS L +P PV+I + L + LL R TAL Sbjct: 132 ILMVAGRGIAQLVTEGQIVTFTSPGLTFIGSGSFLTVPMPVVITAVLLGVTALLVRMTAL 191 Query: 202 GMFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGIIVAADIRGADANNAGLWLE 261 G+ IEAVG++ ++ AGVNT ++++ YV GLCAA+AG++VAADIRGADANNAGLWLE Sbjct: 192 GLMIEAVGVSRLSSAGAGVNTPVVLVAVYVWCGLCAAVAGLVVAADIRGADANNAGLWLE 251 Query: 262 LDAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLSGFPPEMNQVVKAVVVLCVL 321 LDAILAVV+GG SL+GGRF LLLSVVGAL IQ MNTGILLSGF PE N +VKA V++ VL Sbjct: 252 LDAILAVVVGGTSLLGGRFGLLLSVVGALTIQAMNTGILLSGFKPEFNLIVKAGVLMVVL 311 Query: 322 IVQS 325 ++QS Sbjct: 312 LLQS 315 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: 402 Number of extensions: 15 Number of successful extensions: 1 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: 341 Length of database: 354 Length adjustment: 29 Effective length of query: 312 Effective length of database: 325 Effective search space: 101400 Effective search space used: 101400 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 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