Align ABC transporter for D-mannitol and D-mannose, permease component 2 (characterized)
to candidate 3609759 Dshi_3142 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_25890 (276 letters) >FitnessBrowser__Dino:3609759 Length = 275 Score = 159 bits (401), Expect = 8e-44 Identities = 91/279 (32%), Positives = 153/279 (54%), Gaps = 7/279 (2%) Query: 1 MTLQQTRRLQSLLLGTLAWAIAILIFFPIFWMVLTSFKTEIDAFATPPQFIFTPTLENYL 60 MT +Q ++ S + L A ++ PI W+ L +FK+ +D + + FTPTLEN+ Sbjct: 1 MTGKQRKQFWSAVHAVLIIAAMFVMLVPILWIFLAAFKSHVDVYQL--KLFFTPTLENFG 58 Query: 61 HVNE---RSGYFSFAWNSVVISFSATALCLLIAVPAAYSMAFYETQRTKGTLLWMLSTKM 117 V + R G F NS V++ + + IA AAYS + + L+ +L+T+ Sbjct: 59 TVFDDPYRLGEKLF--NSTVVALVTVVIAIPIATLAAYSFSRFRLVGETAMLVVILATQF 116 Query: 118 LPPVGVLMPIYLLAKSFGLLDTRIALIIIYTLINLPIVVWMIYTYFKDIPKDILEAARLD 177 LP V +++P +++ + GLLDTR+ LI++ I +P +WMI + IP D EAA +D Sbjct: 117 LPAVVIILPFFIMFRDIGLLDTRLGLILVNLAIVMPFAIWMIKGFIDGIPLDTEEAAMVD 176 Query: 178 GATLWQEMVRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLTSSKAAPLTALIASYSSPE 237 G++ Q + ++LP+A GL ++ + I+ WNE ++L LT+ A L +A + E Sbjct: 177 GSSRLQVIWNIVLPMAAPGLLTSGIFCFIIAWNEFLFALILTNKDAVTLPIGLALFKGEE 236 Query: 238 GLFWAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK 276 G W LSA + AP+ + + +K V+G++ GAV+ Sbjct: 237 GDLWNLLSAAGIIIMAPMFVLALMIRKYFVQGMTMGAVR 275 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: 258 Number of extensions: 12 Number of successful extensions: 3 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: 275 Length adjustment: 25 Effective length of query: 251 Effective length of database: 250 Effective search space: 62750 Effective search space used: 62750 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