Align D-serine/D-alanine/glycine transporter (characterized)
to candidate 1937132 b3795 predicted transporter (NCBI)
Query= SwissProt::P0AAE0 (470 letters) >FitnessBrowser__Keio:1937132 Length = 461 Score = 350 bits (898), Expect = e-101 Identities = 178/462 (38%), Positives = 276/462 (59%), Gaps = 9/462 (1%) Query: 13 APAEQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMR 72 A + L+R L RHI+LIA+GG IG GLFMG+ T+ AGPS++ Y+I G +FF+MR Sbjct: 2 ADNKPELQRGLEARHIELIALGGTIGVGLFMGAASTLKWAGPSVLLAYIIAGLFVFFIMR 61 Query: 73 AMGELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPD 132 +MGE+L SF+ +A + P+ GY T W+YWF W+ G++++ AI Y QFWFP+ Sbjct: 62 SMGEMLFLEPVTGSFAVYAHRYMSPFFGYLTAWSYWFMWMAVGISEITAIGVYVQFWFPE 121 Query: 133 LSDWVASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTG 192 ++ W+ +L + L+ NLA V+++GE+EFWFAMIK+ I+ +IV+GL ++ F + G Sbjct: 122 MAQWIPALIAVALVALANLAAVRLYGEIEFWFAMIKVTTIIVMIVIGLGVIFFGFGN-GG 180 Query: 193 VEASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSI 252 F++L GG+F G GF I V ++ G+EL+G TA E K+P+ +L A+ + Sbjct: 181 QSIGFSNLTEHGGFFAGGWKGFLTALCIVVASYQGVELIGITAGEAKNPQVTLRSAVGKV 240 Query: 253 PIRIIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSAN 312 RI++FYV A+ VI+++ PW+ + SPFV F +G+ AAA +INFVVLT+A S N Sbjct: 241 LWRILIFYVGAIFVIVTIFPWNEIGSNGSPFVLTFAKIGITAAAGIINFVVLTAALSGCN 300 Query: 313 SGVFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAF 372 SG++S RML+ LA+ P A AK+S+ VP G+ S LL G + Y+ P+ F Sbjct: 301 SGMYSCGRMLYALAKNRQLPAAMAKVSRHGVPVAGVAVSIAILLIGSCLNYIIPNPQRVF 360 Query: 373 TMITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMC----WVCMAFFVF 428 + + S + M W +IL S L +R+ H+ +I P ++ +V MAF + Sbjct: 361 VYVYSASVLPGMVPWFVILISQLRFRR----AHKAAIASHPFRSILFPWANYVTMAFLIC 416 Query: 429 VVVLLTLEDDTRQALLVTPLWFIALGLGWLFIGKKRAAELRK 470 V++ + +DTR +L V ++ +A+ + G R + K Sbjct: 417 VLIGMYFNEDTRMSLFVGIIFMLAVTAIYKVFGLNRHGKAHK 458 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: 675 Number of extensions: 32 Number of successful extensions: 2 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: 461 Length adjustment: 33 Effective length of query: 437 Effective length of database: 428 Effective search space: 187036 Effective search space used: 187036 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