Align D-serine/D-alanine/glycine transporter (characterized)
to candidate PP_4840 PP_4840 D-alanine, beta-alanine, D-serine, glycine permease
Query= SwissProt::P0AAE0 (470 letters) >FitnessBrowser__Putida:PP_4840 Length = 468 Score = 692 bits (1785), Expect = 0.0 Identities = 338/452 (74%), Positives = 386/452 (85%) Query: 13 APAEQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMR 72 A E L+RNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMR Sbjct: 8 ATDEPHLQRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMR 67 Query: 73 AMGELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPD 132 AMGELLLSNL YKSF DF++DLLGPWAGYFTGWTYWFCWVVTG+ADVVAI AY QFWFPD Sbjct: 68 AMGELLLSNLNYKSFIDFSADLLGPWAGYFTGWTYWFCWVVTGIADVVAIAAYTQFWFPD 127 Query: 133 LSDWVASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTG 192 L W+ +L + LLL+LNL TVKMFGE+EFWFA++KIVAI+ L+ GL MV F SP+G Sbjct: 128 LPQWIPALTCVGLLLSLNLVTVKMFGELEFWFALVKIVAILGLVATGLYMVITGFTSPSG 187 Query: 193 VEASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSI 252 A A+LWNDGG FP GL GFFAGFQIAVFAFVGIELVGTTAAE K+PE++LPRAINSI Sbjct: 188 RTAQLANLWNDGGMFPHGLMGFFAGFQIAVFAFVGIELVGTTAAEAKNPERTLPRAINSI 247 Query: 253 PIRIIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSAN 312 PIRII+FYV ALI IM+VTPW VVP KSPFVELFVL GLPAAAS+INFVVLTSAASSAN Sbjct: 248 PIRIIVFYVLALIAIMAVTPWRDVVPGKSPFVELFVLAGLPAAASIINFVVLTSAASSAN 307 Query: 313 SGVFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAF 372 SGVFSTSRML+GL+QEG APKAF KLS R+VPA GL FSC CLL G V++Y+ P+V+ AF Sbjct: 308 SGVFSTSRMLYGLSQEGDAPKAFEKLSSRSVPANGLYFSCTCLLLGAVLIYLVPNVVEAF 367 Query: 373 TMITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFVVVL 432 T++TTVSA+LFMFVWT+IL SYL YRK R LH+ S YKMP G+ MC+VC++FF F++VL Sbjct: 368 TLVTTVSAVLFMFVWTLILLSYLKYRKDRAALHQASNYKMPGGRFMCYVCLSFFAFILVL 427 Query: 433 LTLEDDTRQALLVTPLWFIALGLGWLFIGKKR 464 L+LE DTR AL+VTP+WF+ L + + + +R Sbjct: 428 LSLEADTRSALVVTPIWFVVLAVTYQLVRSRR 459 Lambda K H 0.329 0.141 0.440 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: 763 Number of extensions: 15 Number of successful extensions: 1 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: 468 Length adjustment: 33 Effective length of query: 437 Effective length of database: 435 Effective search space: 190095 Effective search space used: 190095 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