Align D-serine/L-alanine/D-alanine/glycine/D-cycloserine uptake porter of 556 aas, CycA (characterized)
to candidate WP_033100257.1 JG50_RS0106285 amino acid permease
Query= TCDB::M1IW84 (556 letters) >NCBI__GCF_000763315.1:WP_033100257.1 Length = 446 Score = 275 bits (704), Expect = 2e-78 Identities = 156/453 (34%), Positives = 251/453 (55%), Gaps = 21/453 (4%) Query: 16 HLRRDLANRHIQLIAIGGAIGTGLFMGSGRTISLAGPAVMVVYGIIGFFVFFVLRAMGEL 75 HL++ L RH+Q++A+GGAIG G+F GS TIS AGP V+ Y + G ++ V+ AM E+ Sbjct: 4 HLQKQLLPRHVQMMALGGAIGAGIFQGSAETISAAGPGVIFSYALAGILLYIVMSAMAEM 63 Query: 76 LL--SNLNYKSFVDFAADLLGPAAGFFVGWSYWFAWVVTGIADLVAITSYARFWWPGLPI 133 L + + + V A G F +GW Y+ WV+ ++V ++ ++W+ +P+ Sbjct: 64 ALGFAGTDLRGLVHKA---FGTRVSFILGWLYFIQWVLVMAVEIVTAGTFLQYWF-SVPV 119 Query: 134 WVPALVTVALILAVNLFSVRHFGELEFWFALIKVAAIVCLIAVGAILVATNFVSPHGVHA 193 W+ +L+ +I+A+NLFSVR FGE+E+W +K+ ++ + +GA+L+ + P Sbjct: 120 WLLSLIVTLVIIAINLFSVRLFGEIEYWLTSVKIVTLIVFVILGALLLFG--IIPSAQAP 177 Query: 194 TIENLWNDNGFFPTGFLGVVSGFQIAFFAYIGVELVGTAAAETADPRRTLPRAINAVPLR 253 + N GFFP G+ GV+S I F+Y G E++G E D ++TLPR I V LR Sbjct: 178 GLTNYRVHGGFFPLGWQGVLSSLLIVIFSYGGTEMIGLTITEMKDAKKTLPRVIKGVILR 237 Query: 254 VAVFYIGALLAILAVVPWRQFASGESPFVTMFSLAGLAAAASVVNFVVVTAAASSANSGF 313 + +FY+ LL I ++PW Q S SPFV + S GL A+++NF+++TA S+ANSG Sbjct: 238 ICLFYVLPLLIITGLIPWDQVKSSGSPFVEVLSAVGLKGVANIMNFILLTAVISAANSGM 297 Query: 314 FSTGRMLFGLADEGHAPAAFHQLNRGGVPAPALLLTAP-LLLTSIPLLYAGRSVIGAFTL 372 ++T RML+ LA E APA F +L + GVP AL ++ L L S+ A SV F Sbjct: 298 YATTRMLYSLAGEKEAPAFFTRLGKRGVPIYALAASSVCLFLGSLVAFIAPESV---FQY 354 Query: 373 VTTVSSLLFMFVWAMIIISYLVYRRRHPQRHTD---SVYKMPGGVVMCWAVLVFFAFVIW 429 + + + W +I +S+L R ++ +R D S + G+ + +V A +I+ Sbjct: 355 LMGIPGYTVILTWILICLSHLKLRGKY-ERTPDFRLSFFPFTTGITL----IVLAAIMIF 409 Query: 430 TLTTETETATALAWFPLWFVL-LAVGWLVTQRR 461 L + + + + VL +A WL +R Sbjct: 410 VLLSPKNLINTIVYLAIILVLTIASQWLKPNQR 442 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: 525 Number of extensions: 29 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: 446 Length adjustment: 34 Effective length of query: 522 Effective length of database: 412 Effective search space: 215064 Effective search space used: 215064 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