Align D-serine/L-alanine/D-alanine/glycine/D-cycloserine uptake porter of 556 aas, CycA (characterized)
to candidate WP_009490041.1 C683_RS03460 amino acid permease
Query= TCDB::M1IW84 (556 letters) >NCBI__GCF_000313915.1:WP_009490041.1 Length = 479 Score = 271 bits (694), Expect = 3e-77 Identities = 156/425 (36%), Positives = 237/425 (55%), Gaps = 25/425 (5%) Query: 17 LRRDLANRHIQLIAIGGAIGTGLFMGSGRTISLAGPA-VMVVYGIIGFFVFFVLRAMGEL 75 ++R L RH+ +IAIGG+IGTGLF+ SG IS AGP +V YG+IG VFF++ ++GE+ Sbjct: 8 MQRGLKTRHLSMIAIGGSIGTGLFVASGSAISTAGPGGALVAYGLIGLLVFFMMTSLGEM 67 Query: 76 LLSNLNYKSFVDFAADLLGPAAGFFVGWSYWFAWVVTGIADLVAITSYARFWWPGLPIWV 135 SF +A + PA GF +GW+YWF W +T D+ +W+P +P W+ Sbjct: 68 ATYMPVSGSFSTYATKFVDPAFGFALGWNYWFNWAITLAVDISTSAIIMEYWFPDVPGWI 127 Query: 136 PALVTVALILAVNLFSVRHFGELEFWFALIKVAAIVCLIAVGAILVATNFVSPHGVHATI 195 +++ LI +NL SV FGE EFWF++IKV ++C I VG +L T + H + Sbjct: 128 FSIIFFVLIFLMNLASVELFGEAEFWFSMIKVITVICFIGVG-LLTVTGILGGHA--DGL 184 Query: 196 ENLWNDNGFFPTGFLGVVSGFQIAFFAYIGVELVGTAAAETADPRRTLPRAINAVPLRVA 255 N + F G +VS F +A F++ GVE++G A E+A+P +++P+AI V R+ Sbjct: 185 MNFTKGDAPFVGGLPTIVSVFVVAGFSFQGVEMIGITAGESANPEKSIPKAIKQVFWRIL 244 Query: 256 VFYIGALLAILAVVPWRQ--------FASGESPFVTMFSLAGLAAAASVVNFVVVTAAAS 307 +FY+ ++ I ++P+ SPF +F AGLAAAASV+N V++T+ S Sbjct: 245 LFYLVSIFIIGLIIPYTSPNLLGSDATDIAISPFTLVFQRAGLAAAASVMNAVILTSVLS 304 Query: 308 SANSGFFSTGRMLFGLADEGHAPAAFHQLNRGGVPAPALLLTAPLLLTSIPLLYAGRSVI 367 + NSG ++ RML +A G AP AF ++NR G+P ALLLTA + + + G + Sbjct: 305 AGNSGLYAGARMLCAMAQSGQAPKAFQKINRRGIPVNALLLTAAVGGLAFITSFMGDKI- 363 Query: 368 GAFTLVTTVSSLLFMFVWAMIIISYLVYRRRH-PQRHTDSVYK-----MPGG----VVMC 417 + + + S L W + +S+ +RR Q H S K P G ++MC Sbjct: 364 --YNFLLSASGLTGFIAWFGVAVSHYRFRRAFIKQGHDISELKYKSKWFPFGPIFAIIMC 421 Query: 418 WAVLV 422 AV+V Sbjct: 422 IAVIV 426 Lambda K H 0.328 0.140 0.442 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: 629 Number of extensions: 39 Number of successful extensions: 5 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: 556 Length of database: 479 Length adjustment: 35 Effective length of query: 521 Effective length of database: 444 Effective search space: 231324 Effective search space used: 231324 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: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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