Align ABC transporter for D-mannitol and D-mannose, permease component 2 (characterized)
to candidate AO353_25125 AO353_25125 sugar ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_25890 (276 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25125 Length = 280 Score = 151 bits (382), Expect = 1e-41 Identities = 95/278 (34%), Positives = 149/278 (53%), Gaps = 10/278 (3%) Query: 7 RRLQSLLLGTLAWA-IAILIF---FPIFWMVLTSFKTEIDAFATPPQFIFTPTLENYLHV 62 R L+ LL W I IL+ FP ++ ++TS K F +I +P NY V Sbjct: 4 RLLKKALLRLGFWCLIGILLLYAVFPFYYAIVTSLKPSSALFEVS-YWIDSPDFSNYAAV 62 Query: 63 NERSGYFSFAWNSVVISFSATALCLLIAVPAAYSMAFYETQRTKGTLLWM-LSTKMLPPV 121 +S + NS+V++ L L +++ AAY++ + R +GT+L M L M P V Sbjct: 63 LHQSSFLRAIGNSLVVALCVVTLALFLSLTAAYALGRVKF-RGRGTVLMMVLGVSMFPQV 121 Query: 122 GVLMPIYLLAKSFGLLDTRIALIIIYTLINLPIVVWMIYTYFKDIPKDILEAARLDGATL 181 VL ++ + ++ GL +T ALI+ YT+ LP VW++ T+ +P ++ EAA +DGA+ Sbjct: 122 AVLSGLFEVIRALGLYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGASP 181 Query: 182 WQEMVRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLT---SSKAAPLTALIASYSSPEG 238 W + RVLLP+ L +T LL+ I WNE ++L T + + P+ + S SP Sbjct: 182 WVTLTRVLLPLLWPALVTTGLLAFIAAWNEFLFALTFTLTDTQRTVPVAIALISGGSPHE 241 Query: 239 LFWAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK 276 L W L A S L P++I I Q+++V GL+ GA+K Sbjct: 242 LPWGLLMAASVLVTVPLVILVLIFQRRIVSGLTAGALK 279 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: 222 Number of extensions: 9 Number of successful extensions: 2 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: 276 Length of database: 280 Length adjustment: 25 Effective length of query: 251 Effective length of database: 255 Effective search space: 64005 Effective search space used: 64005 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