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) >FitnessBrowser__Putida:PP_4840 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:
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