Align D-serine/L-alanine/D-alanine/glycine/D-cycloserine uptake porter of 556 aas, CycA (characterized)
to candidate WP_034528196.1 LOSG293_RS05960 amino acid permease
Query= TCDB::M1IW84 (556 letters) >NCBI__GCF_000740055.1:WP_034528196.1 Length = 498 Score = 269 bits (687), Expect = 2e-76 Identities = 149/398 (37%), Positives = 226/398 (56%), Gaps = 18/398 (4%) Query: 11 TDTQPH-LRRDLANRHIQLIAIGGAIGTGLFMGSGRTISLAGPA-VMVVYGIIGFFVFFV 68 T+ + H ++R L RH+ +IA+GG IGTGLF+ SG IS AGP +V Y +G V+F+ Sbjct: 10 TELENHEVKRGLKTRHVSMIALGGCIGTGLFVASGSAISSAGPGGALVAYIAMGMMVYFL 69 Query: 69 LRAMGELLLSNLNYKSFVDFAADLLGPAAGFFVGWSYWFAWVVTGIADLVAITSYARFWW 128 + ++GE+ + SF ++A + PA GF +GW+YWF W +T D+ +FW Sbjct: 70 MTSLGEMATNMPISGSFAAYSAKYVDPALGFAMGWNYWFNWAITVAVDISTAALVIKFWL 129 Query: 129 PGLPIWVPALVTVALILAVNLFSVRHFGELEFWFALIKVAAIVCLIAVGAILVATNFVSP 188 PG+P W+ + V + ++ +N SVR +GE EFW +LIK+ IV + VG + + Sbjct: 130 PGVPGWIWSAVALVILFVINALSVRTYGETEFWLSLIKIVTIVVFLVVGLLTI----FGI 185 Query: 189 HGVHAT-IENLWNDNGFFPTGFLGVVSGFQIAFFAYIGVELVGTAAAETADPRRTLPRAI 247 G HAT +EN F GF ++S F +A F++ G ELVG A E+ DP +++P+AI Sbjct: 186 MGGHATGLENFTYKKAPFVGGFPAILSVFVVAGFSFQGTELVGITAGESEDPHKSVPKAI 245 Query: 248 NAVPLRVAVFYIGALLAILAVVPWRQF--------ASGESPFVTMFSLAGLAAAASVVNF 299 N V R+ +FYI A+ I ++P+ SPF +F AGLAAAAS++N Sbjct: 246 NQVFWRIILFYILAIAVIALIIPYTSHDLLGSSATDVAISPFTLVFQRAGLAAAASIMNA 305 Query: 300 VVVTAAASSANSGFFSTGRMLFGLADEGHAPAAFHQLNRGGVPAPALLLTAPLLLTSIPL 359 V++T+ SSANSG +++ RML+ LA EG+AP AF + + G+P AL+ T + + Sbjct: 306 VILTSVLSSANSGMYASTRMLYSLAHEGYAPKAFGRTTKNGIPMLALVGTTLIAAVTFIS 365 Query: 360 LYAGRSVIGAFTLVTTVSSLLFMFVWAMIIISYLVYRR 397 AG + + + S L W I IS+ +RR Sbjct: 366 SIAGPQL---YLWLVAASGLTGFIAWIGIAISHFRFRR 400 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: 692 Number of extensions: 48 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: 556 Length of database: 498 Length adjustment: 35 Effective length of query: 521 Effective length of database: 463 Effective search space: 241223 Effective search space used: 241223 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