Align D-mannitol and D-mannose transporter (MFS superfamily) (characterized)
to candidate WP_057509309.1 ABB28_RS14540 glucose/galactose MFS transporter
Query= reanno::SB2B:6936374 (413 letters) >NCBI__GCF_001431535.1:WP_057509309.1 Length = 429 Score = 169 bits (428), Expect = 1e-46 Identities = 131/419 (31%), Positives = 198/419 (47%), Gaps = 40/419 (9%) Query: 14 AAPAQSHQQLLFGAMTSLFFIWGFITALNDILIPHLKGIFDLSYTQAMLVQFCFFGAYFL 73 AA A++ + LFF+ GF T LN LI +K F+L A LV F+ +YF Sbjct: 6 AAGARTSVTTSIAIVGVLFFLIGFFTWLNGPLITFVKLAFELDEVGAFLVLMVFYLSYFF 65 Query: 74 VSPLAGVLIARIGYLRGIIFGLSTMATGCLLFYPASSLEQYALFLLALFVLASGITILQV 133 ++ + ++ R G +G+ L MA G F ++ Y L LF++ SG+ +LQ Sbjct: 66 LALPSSWILRRTGMKKGLSLSLLVMAAGAATFGEFATQRWYPGALGGLFIIGSGLALLQT 125 Query: 134 SANPFVARLGPERTAASRLNLAQALNSLGHTLGP-LFGSLLIFG----------AAAGTH 182 + NP+++ LGP TAA R+ L N + L P L G+L++ G A T Sbjct: 126 AINPYISILGPIETAARRIALMGICNKVAGMLAPVLIGTLVLHGVGDLSTAVEQADVATR 185 Query: 183 EA--------VQLPYLLLAAVIGIIAVGFIF------LGGKVKHADMGVDHRHKGSLLSH 228 A + PYL +AA++ +++V +F + A G + S+ Sbjct: 186 AALLNDFAAKIHAPYLGMAALLVVLSVAVLFSPLPELKSSEANAAPAGKGGIERSSIFQF 245 Query: 229 KRLLLGALAIFLYVGAEVSIGSFLVNY---FAEPSIGGLDEKSAAELVSWYWGGAMIGRF 285 L LG L +F+YVG EV G + Y F P LD+ S G ++G Sbjct: 246 PHLWLGVLCLFVYVGVEVMAGDAIGTYGHGFDLP----LDQTKM--FTSLTLGAMLVGYV 299 Query: 286 AGAALTRRF-NPAMVLAANAVFANLLLMLTIVSSGELALVAVLAVGFFNSIMFPTIFTLA 344 G L RF + + L+ +A L + + G +++ V +GF N++M+P IF LA Sbjct: 300 VGLLLIPRFVSQSRYLSISASLGVLFCVGAYFTHGYVSVAFVALLGFANAMMWPAIFPLA 359 Query: 345 IEGLGELTSRGSGLLCQAIVGGALLPVIQGVVADNVGVQLSFI---VPTFCYFYICWYA 400 I GLG T GS LL I GGA++P V+ +V QL F+ VP CY YI +Y+ Sbjct: 360 IRGLGRFTETGSALLVMGIAGGAIIPQAFAVLKQHVDFQLVFLLLMVP--CYLYILFYS 416 Lambda K H 0.329 0.142 0.425 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: 460 Number of extensions: 26 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: 413 Length of database: 429 Length adjustment: 32 Effective length of query: 381 Effective length of database: 397 Effective search space: 151257 Effective search space used: 151257 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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