Align ABC transporter for D-mannitol and D-mannose, permease component 2 (characterized)
to candidate AZOBR_RS25590 AZOBR_RS25590 sugar ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_25890 (276 letters) >FitnessBrowser__azobra:AZOBR_RS25590 Length = 277 Score = 137 bits (344), Expect = 3e-37 Identities = 87/269 (32%), Positives = 146/269 (54%), Gaps = 11/269 (4%) Query: 12 LLLGTLAWAIAILIFFPIFWMVLTSFKTEIDAFATPPQFIFTPTLENYLHVNERSGYFSF 71 L+LG +AWA+ FP W ++TS K A T + P+L NY + + + Sbjct: 15 LVLGIVAWAV-----FPFAWAIVTSLKAG-SALFTVEAWPSQPSLANYAAIFKEQPFGRN 68 Query: 72 AWNSVVISFSATALCLLIAVPAAYSMAFYETQRTKGTLLWM-LSTKMLPPVGVLMPIYLL 130 NS++ + + AL L +AV AAY++ R +G LL++ L M P V VL ++ L Sbjct: 69 ILNSLLAASAVVALSLGLAVLAAYALGRVRF-RGRGLLLFVVLGVSMFPQVAVLSGLFEL 127 Query: 131 AKSFGLLDTRIALIIIYTLINLPIVVWMIYTYFKDIPKDILEAARLDGATLWQEMVRVLL 190 + GL + +L++ Y + LP VW++ T+ +++PK++ EAA +DGA + + RV L Sbjct: 128 VRWLGLYNRIGSLVLSYLIFTLPFTVWVLTTFMRELPKELEEAAMVDGAGPFVIVTRVFL 187 Query: 191 PIAKGGLASTVLLSLILCWNEAFWSLNLT---SSKAAPLTALIASYSSPEGLFWAKLSAV 247 P+ LA+T LL+ I WNE ++L T ++ P+ + S +S L W ++ A Sbjct: 188 PLMGPALAATGLLAFIAAWNEFLFALTFTLTDDARTVPVAIALMSGASQYELPWGQIMAA 247 Query: 248 STLACAPILIFGWISQKQLVRGLSFGAVK 276 S + P++ + Q+++V GL+ GAVK Sbjct: 248 SVVVTVPLIGLVLLFQRRIVSGLTAGAVK 276 Lambda K H 0.327 0.138 0.431 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: 209 Number of extensions: 10 Number of successful extensions: 5 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: 276 Length of database: 277 Length adjustment: 25 Effective length of query: 251 Effective length of database: 252 Effective search space: 63252 Effective search space used: 63252 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 (21.8 bits) S2: 47 (22.7 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