Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate PP_4840 PP_4840 D-alanine, beta-alanine, D-serine, glycine permease
Query= uniprot:A0A0C4YRF7 (472 letters) >FitnessBrowser__Putida:PP_4840 Length = 468 Score = 451 bits (1161), Expect = e-131 Identities = 217/450 (48%), Positives = 313/450 (69%), Gaps = 4/450 (0%) Query: 15 EEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRAL 74 +E L R L +RHIQ+IAIGGAIG GLF+G+G+ I++AGP ++ Y I G +FF+MRA+ Sbjct: 10 DEPHLQRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAM 69 Query: 75 GELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVP 134 GELLL SF ++ + +GP+AG+ TGW+YWF WVVTG+A++ A+A Y +WFPD+P Sbjct: 70 GELLLSNLNYKSFIDFSADLLGPWAGYFTGWTYWFCWVVTGIADVVAIAAYTQFWFPDLP 129 Query: 135 QWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVT-PLGPT 193 QWIPAL + +L +N V V +FGELEFWFAL+K+V I+ ++ GL ++ G T P G T Sbjct: 130 QWIPALTCVGLLLSLNLVTVKMFGELEFWFALVKIVAILGLVATGLYMVITGFTSPSGRT 189 Query: 194 ASFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVW 253 A +NLW GG P G +G QI +FA+ G+EL+G TA EA+NPE+ LP A N + Sbjct: 190 AQLANLWNDGGMFPHGLMGFFAGFQIAVFAFVGIELVGTTAAEAKNPERTLPRAINSIPI 249 Query: 254 RILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSG 313 RI++FYV ALI +MA+ PW ++ PG SPFV +F G+P AA+I+N VV+T+AASS NSG Sbjct: 250 RIIVFYVLALIAIMAVTPWRDVVPGKSPFVELFVLAGLPAAASIINFVVLTSAASSANSG 309 Query: 314 IFSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPE--QVFVW 371 +FST RMLY L+Q G AP+AF ++SS+ VP+ + FS + +G +L Y+VP + F Sbjct: 310 VFSTSRMLYGLSQEGDAPKAFEKLSSRSVPANGLYFSCTCLLLGAVLIYLVPNVVEAFTL 369 Query: 372 VTSISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLL 431 VT++S V ++ W++I++++L YRK AA +A ++MPG + ++ ++F + VLL Sbjct: 370 VTTVSAVLFMFVWTLILLSYLKYRKDRAALH-QASNYKMPGGRFMCYVCLSFFAFILVLL 428 Query: 432 SLDPGTRVALYVAPVWFALLGIGYRFTKSR 461 SL+ TR AL V P+WF +L + Y+ +SR Sbjct: 429 SLEADTRSALVVTPIWFVVLAVTYQLVRSR 458 Lambda K H 0.328 0.142 0.445 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: 698 Number of extensions: 28 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: 472 Length of database: 468 Length adjustment: 33 Effective length of query: 439 Effective length of database: 435 Effective search space: 190965 Effective search space used: 190965 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