Align Serine transporter, SerP2 or YdgB, of 459 aas and 12 TMSs (Trip et al. 2013). Transports L-alanine (Km = 20 μM), D-alanine (Km = 38 μM), L-serine, D-serine (Km = 356 μM) and glycine (Noens and Lolkema 2015). The encoding gene is adjacent to the one encoding SerP1 (TC# 2.A.3.1.21) (characterized)
to candidate PP_4840 PP_4840 D-alanine, beta-alanine, D-serine, glycine permease
Query= TCDB::F2HQ24 (457 letters) >lcl|FitnessBrowser__Putida:PP_4840 PP_4840 D-alanine, beta-alanine, D-serine, glycine permease Length = 468 Score = 362 bits (930), Expect = e-104 Identities = 189/438 (43%), Positives = 276/438 (63%), Gaps = 6/438 (1%) Query: 13 QRGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALMYILLRAIGEMLY 72 QR L NRHIQLIAI G IGTGLF+G+GK+I L GPSIIFVY+IIG +++ ++RA+GE+L Sbjct: 15 QRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMGELLL 74 Query: 73 QDPNQHSFLNFVSRYLGEKPGYFIQWSYLLVVVFVAMAELIAIGTYINFWLPDLPIWMTE 132 + N SF++F + LG GYF W+Y V +A+++AI Y FW PDLP W+ Sbjct: 75 SNLNYKSFIDFSADLLGPWAGYFTGWTYWFCWVVTGIADVVAIAAYTQFWFPDLPQWIPA 134 Query: 133 VFVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLILTAIILIFSHYHTGTD-TVSVTN 191 + + LL LN + K FGE EFWF ++KIVAI+GL+ T + ++ + + + + T + N Sbjct: 135 LTCVGLLLSLNLVTVKMFGELEFWFALVKIVAILGLVATGLYMVITGFTSPSGRTAQLAN 194 Query: 192 ITKGFEFFPNGLSNFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKAINQIPIRIVLF 251 + FP+GL FF FQ+ +FAFV +E +G TAAE NP TL +AIN IPIRI++F Sbjct: 195 LWNDGGMFPHGLMGFFAGFQIAVFAFVGIELVGTTAAEAKNPERTLPRAINSIPIRIIVF 254 Query: 252 YVGALLAIMSIYQWRDIPADKSPFVTIFQLIGIKWAAALVNFVVLTSAASALNSALFSIT 311 YV AL+AIM++ WRD+ KSPFV +F L G+ AA+++NFVVLTSAAS+ NS +FS + Sbjct: 255 YVLALIAIMAVTPWRDVVPGKSPFVELFVLAGLPAAASIINFVVLTSAASSANSGVFSTS 314 Query: 312 RNLYSLSKLNNDKILKPFTKFSKAGVPVNALLFT-SLLILFTPFISMIPAISNSFVFITS 370 R LY LS+ + K F K S VP N L F+ + L+L I ++P + +F +T+ Sbjct: 315 RMLYGLSQEGDAP--KAFEKLSSRSVPANGLYFSCTCLLLGAVLIYLVPNVVEAFTLVTT 372 Query: 371 VATNLFLVVYLMTLITYLKYRK--SSDFDPKGFVLPAAHIFIPLAIAGFVLIFISLFCFK 428 V+ LF+ V+ + L++YLKYRK ++ + +P + ++ F I + L Sbjct: 373 VSAVLFMFVWTLILLSYLKYRKDRAALHQASNYKMPGGRFMCYVCLSFFAFILVLLSLEA 432 Query: 429 DTIVPAIGSVIWVLIFGL 446 DT + + IW ++ + Sbjct: 433 DTRSALVVTPIWFVVLAV 450 Lambda K H 0.330 0.144 0.431 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: 605 Number of extensions: 30 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: 457 Length of database: 468 Length adjustment: 33 Effective length of query: 424 Effective length of database: 435 Effective search space: 184440 Effective search space used: 184440 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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