Align D-serine/D-alanine/glycine transporter (characterized)
to candidate 14540 b0402 predicted cryptic proline transporter (NCBI)
Query= SwissProt::A0A0H2VDI7 (470 letters) >FitnessBrowser__Keio:14540 Length = 457 Score = 366 bits (940), Expect = e-106 Identities = 186/449 (41%), Positives = 282/449 (62%), Gaps = 10/449 (2%) Query: 15 AEQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAM 74 ++ L+R L+ RHI+ +A+G AIGTGLF GS I +AGPS++ Y+I G + +MRA+ Sbjct: 3 SKNKLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGIAAYIIMRAL 62 Query: 75 GELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPGLS 134 GE+ + N SFS +A + LGP AGY TGWTY F ++ +ADV A Y WFP + Sbjct: 63 GEMSVHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPTVP 122 Query: 135 DWVASLSVIILLLVLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQS---PT 191 W+ LSV++++ +NL +VK+FGE+EFWF+ K+ I+ +IV G ++ + PT Sbjct: 123 HWIWVLSVVLIICAVNLMSVKVFGELEFWFSFFKVATIIIMIVAGFGIIIWGIGNGGQPT 182 Query: 192 GVEASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINS 251 G+ +LW++GG+F G G Q+ +FA+ GIE++G TA E KDPEKS+PRAINS Sbjct: 183 GIH----NLWSNGGFFSNGWLGMVMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINS 238 Query: 252 IPIRIIMFYVFSLIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSA 311 +P+RI++FYV +L VIMS+ PW+ V SPFV F +G+ AAS++NFVVLT++ S+ Sbjct: 239 VPMRILVFYVGTLFVIMSIYPWNQVGTAGSPFVLTFQHMGITFAASILNFVVLTASLSAI 298 Query: 312 NSGVFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGA 371 NS VF RML G+A++G APK F+K S+R +P + LL V + Y+ P Sbjct: 299 NSDVFGVGRMLHGMAEQGSAPKIFSKTSRRGIPWVTVLVMTTALLFAVYLNYIMPE--NV 356 Query: 372 FTMITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSI-YKMPLGKLMCWVCMAFFVFVL 430 F +I +++ ++VW +IL S + +R++ P K++ +K+P G + F +F++ Sbjct: 357 FLVIASLATFATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVATTIGGLIFLLFII 416 Query: 431 VLLTLEDDTRQALLVTPLWFIALGLGWLF 459 L+ DTR +L V W + L +GW+F Sbjct: 417 GLIGYHPDTRISLYVGFAWIVVLLIGWMF 445 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: 666 Number of extensions: 40 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: 457 Length adjustment: 33 Effective length of query: 437 Effective length of database: 424 Effective search space: 185288 Effective search space used: 185288 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