Align D-serine/D-alanine/glycine transporter (characterized)
to candidate Pf6N2E2_4195 transport permease protein of gamma-aminobutyrate
Query= SwissProt::A0A0H2VDI7 (470 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4195 Length = 464 Score = 267 bits (683), Expect = 5e-76 Identities = 141/450 (31%), Positives = 246/450 (54%), Gaps = 5/450 (1%) Query: 19 LRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMGELL 78 L + L RH+ +++I G IG GLF+GSG I+ AGP+++ Y G ++ VMR +GE+ Sbjct: 10 LEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGPAVLLAYAAAGALVVLVMRMLGEMA 69 Query: 79 LSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPGLSDWVA 138 +++ + SFS +A +G WAG+ GW YW+ WV+ + A WFP ++ W Sbjct: 70 VASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHAWFPNVAIWAF 129 Query: 139 SLSVIILLLVLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGVEASFA 198 +L + +LL V NL +VK +GE EFWFA++K+VAI+ I GL ++A+ PT + + Sbjct: 130 TLVITLLLTVTNLFSVKNYGEFEFWFALVKVVAIIGFI--GLGVMAIFGVLPTSQVSGVS 187 Query: 199 HLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPIRIIM 258 HL++ G+ P G+ +F+F+G E+V AAE+K+P + + +A NS+ RI + Sbjct: 188 HLFDTQGFLPNGMGAVLGAILTTMFSFMGTEIVTIAAAESKNPGQQISKATNSVIWRIGL 247 Query: 259 FYVFSLIVIMSVTPWSS-VVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSGVFS 317 FY+ S+ +++++ PW+ ++ + + +G+P A +++ VVL + S NS +++ Sbjct: 248 FYLVSIFIVVALVPWNDPLLASVGSYQTVLERMGIPNAKLIVDIVVLVAVTSCLNSALYT 307 Query: 318 TSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAFTMITT 377 SRM+F L + G AP + +K P + S V YV P+ + F + Sbjct: 308 ASRMMFSLGKRGDAPAVSQRTNKSGTPYWAVMLSTGAAFLAVFANYVAPAAV--FDFLLA 365 Query: 378 VSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFVLVLLTLED 437 S + + V+ +I S L RKQR EK + M L + + + F V L ++ ++ Sbjct: 366 SSGAIALLVYLVIAVSQLRMRKQRMARGEKVAFSMWLFPGLTYAVIVFIVGALTIMLFQE 425 Query: 438 DTRQALLVTPLWFIALGLGWLFIGKKRAAE 467 R +L T L + + + + + ++R A+ Sbjct: 426 AHRVEILATGLLSVLVVISGVLVQRRRIAK 455 Lambda K H 0.329 0.141 0.441 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: 560 Number of extensions: 31 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: 470 Length of database: 464 Length adjustment: 33 Effective length of query: 437 Effective length of database: 431 Effective search space: 188347 Effective search space used: 188347 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: 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