Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate BPHYT_RS22690 BPHYT_RS22690 D-galactonate transporter
Query= reanno::WCS417:GFF828 (454 letters) >FitnessBrowser__BFirm:BPHYT_RS22690 Length = 458 Score = 394 bits (1012), Expect = e-114 Identities = 199/434 (45%), Positives = 271/434 (62%), Gaps = 13/434 (2%) Query: 10 RYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAGQIPGGW 69 RY IL +L + T INY DR + IA L K+LGI+A +G +FS F W+YVA QIPGG Sbjct: 29 RYQILALLAVGTMINYLDRTVLGIAAPQLTKELGINAALMGLLFSVFSWSYVASQIPGGL 88 Query: 70 LLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAEAPSFPGNAR 129 LDRFGSK Y LS+ WSL T+ QG V G ALF R +G++EAP FP N+R Sbjct: 89 FLDRFGSKLTYFLSMTLWSLCTLAQGLVHGIG------ALFAFRLGLGVSEAPCFPTNSR 142 Query: 130 IVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVIGIIFSLIW 189 +VA WFP +ER A+ + +Y F+P + ++ +FGW+ +F V+G +GI+F IW Sbjct: 143 VVATWFPQSERAMATGTYTVGEYIGLAFFSPFLFMLMGAFGWRSLFYVVGGVGIVFGGIW 202 Query: 190 LKVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGKG-------KKTDGPKWDYIRQLLT 242 PR HP N+AE ++I A G + +D K+ G +W I +LL Sbjct: 203 WMFYREPRDHPSANQAELDYIEAGGGLTHRKKDADSAGGADAASAKSGGFEWRTIGRLLK 262 Query: 243 NRMMLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLGGV 302 +R + G+ LGQ+ N FFLTWFP YL +R M LK GF A +P I IG + GG Sbjct: 263 HRQLTGICLGQFAGNSTLVFFLTWFPTYLATERHMAWLKIGFFAIMPFIAASIGVMFGGF 322 Query: 303 ISDYLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGALGW 362 SD+LLR+G S ARK PII GLL++S+I+ NYV+ V+ +++AFF +G+ ALGW Sbjct: 323 FSDWLLRRGKSPNVARKLPIIAGLLLASTIILANYVESNVAVIAILSVAFFAQGMAALGW 382 Query: 363 AVVSDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVAVF 422 +VSD +P + G++GG+FN NLA I TP+V+G+I++ TGSF ALVF+GA AL+ Sbjct: 383 TLVSDIAPDGLLGVTGGIFNFAANLAGIVTPLVVGFIVAATGSFVGALVFIGAIALIGAL 442 Query: 423 SYLVIVGPIKRVVL 436 SY+ IVG IKR+VL Sbjct: 443 SYIFIVGDIKRIVL 456 Lambda K H 0.327 0.142 0.444 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: 704 Number of extensions: 33 Number of successful extensions: 4 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: 454 Length of database: 458 Length adjustment: 33 Effective length of query: 421 Effective length of database: 425 Effective search space: 178925 Effective search space used: 178925 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: 51 (24.3 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