Align Glucose-6-P:Pi antiporter, Hpt (may also transport other organophosphates including C3 organophosphates) (characterized)
to candidate 6939142 Sama_3240 putative regulatory protein UhpC (RefSeq)
Query= TCDB::Q9Z7N9 (455 letters) >FitnessBrowser__SB2B:6939142 Length = 445 Score = 216 bits (549), Expect = 2e-60 Identities = 132/438 (30%), Positives = 221/438 (50%), Gaps = 29/438 (6%) Query: 21 EVVKKKYKYWRIRIFYSMFIGYIFYYFTRKSFTFAMPTLIADLGFDKAQLGIIGSTLYFS 80 E ++ YK ++ ++F + +GY +Y R S A ++ +LGIIGS + + Sbjct: 19 EKIRSIYKKYQWQVFLGLVLGYAMFYVARMSLNVAKKPMLDAGIVTLDELGIIGSAFFLT 78 Query: 81 YGISKFVSGVMSDQSNPRYFMAIGLMITGLTNIFFGMSSSIVLFALWWGLNGWFQGWGWP 140 Y + KF +G +SD +N FM++ L ++ +T +F GM+++ F L W +NGWFQ G Sbjct: 79 YAVGKFSNGFLSDYANIGRFMSVSLGLSAITCLFMGMNTATFFFILLWAMNGWFQSVGSA 138 Query: 141 PCARLLTHWYAKSERGTWWSVWSTSHNIGGALIPILTGFIIDYSGWRGAMYVPGILCIGM 200 P + W++ +RG+ +S+W S NIG + ILT ++ + GWR GI Sbjct: 139 PSCVSIFQWFSPKQRGSVYSIWGGSRNIGEGITWILTATVVSFFGWRAGFVGAGIATFAA 198 Query: 201 GLVLINRLRDTPQSLGLPPIEKYKRDPHHAHHEGKSASEGTEEIERELSTREI--LFTYV 258 + + L+D PQ+ GLP +P A+ E EI++++ +EI ++ Sbjct: 199 AIAMYFVLKDRPQTYGLP-------EPAVAYGE-------DAEIKKKVDPKEIRRAQLFI 244 Query: 259 LTNQWLWFLAAASFFIYIVRMAVNDWSALFLIETKHYAAVKANFCVSLFEIGGLFGMLVA 318 L +W +A A +YI R A++ W+ L+L E K Y+ + A F +S + I G G ++A Sbjct: 245 LKQPTVWIIALACAAMYISRYAMSSWAVLYLQEEKGYSLIDAGFAMSAYPIAGFAGAILA 304 Query: 319 GWLSDKISKGNRGPMNVLFSLGLLFAI-LGMWFSRSHNQWWVDGTLLFVIGFFLYGPQMM 377 G +SDK+ NR +L+ L + + L W +S +D L +IG+ + G + Sbjct: 305 GIISDKVFNANRHIPTLLYGLANIAGLCLMFWGPQSR---VMDAVALGLIGYAIGGLVVF 361 Query: 378 I-GLAAAELSHKKAAGTASGFTGWFAYFGAT---FAGYPLGKVTDVWGWKGFFIAL---- 429 + GL A +L K A G GF G +Y A+ L K+ +V G K + + Sbjct: 362 LAGLTACDLMPKTAVGAVKGFIGLCSYIAASAQEIVSASLIKIHEVDGVKHYDFSTAQYF 421 Query: 430 -LACASIALLLFLPTWNA 446 LA A +++ L + WNA Sbjct: 422 WLAAAVVSMFLAMSVWNA 439 Lambda K H 0.327 0.141 0.476 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: 726 Number of extensions: 46 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: 455 Length of database: 445 Length adjustment: 33 Effective length of query: 422 Effective length of database: 412 Effective search space: 173864 Effective search space used: 173864 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