Align D-serine/L-alanine/D-alanine/glycine/D-cycloserine uptake porter of 556 aas, CycA (characterized)
to candidate WP_033101984.1 JG50_RS0115245 amino acid permease
Query= TCDB::M1IW84 (556 letters) >NCBI__GCF_000763315.1:WP_033101984.1 Length = 484 Score = 254 bits (650), Expect = 4e-72 Identities = 162/461 (35%), Positives = 256/461 (55%), Gaps = 25/461 (5%) Query: 15 PHLRRDLANRHIQLIAIGGAIGTGLFMGSGRTISLAGPA-VMVVYGIIGFFVFFVLRAMG 73 P L+R L RH+ +IAIGG+IGTG+F+ SG +IS AGP +V Y IG V+F++ ++G Sbjct: 8 PELKRGLKARHLSMIAIGGSIGTGVFLASGASISEAGPGGALVAYLAIGIMVYFLMTSLG 67 Query: 74 ELLLSNLNYKSFVDFAADLLGPAAGFFVGWSYWFAWVVTGIADLVAITSYARFWWPGLPI 133 E+ SF +A + PA GF +GW+YW+ W +T +L A + +W+P P Sbjct: 68 EMATFMPVAGSFSTYAGRFVDPALGFAMGWNYWYNWAITIAVELSAGSLIMDYWFPHSPS 127 Query: 134 WVPALVTVALILAVNLFSVRHFGELEFWFALIKVAAIVCLIAVGAILVATNFVSPHGVHA 193 + + + + L+ +N SV+ +GE E+WF+ IKVA ++ I +G +++ F G Sbjct: 128 ILWSALFLLLMFGLNALSVKGYGESEYWFSFIKVATVIIFIVIGLLMI---FGIMGGEAI 184 Query: 194 TIENLWNDNGFFPTGFLGVVSGFQIAFFAYIGVELVGTAAAETADPRRTLPRAINAVPLR 253 +N ++ F G+LG++S F IA F++ G ELVG AA E+ +PR+ +P+AI V R Sbjct: 185 GFKNFTINDAPFHHGWLGILSVFMIAGFSFQGTELVGVAAGESENPRKNVPKAIRQVFWR 244 Query: 254 VAVFYIGALLAILAVVPWR--QFASGE------SPFVTMFSLAGLAAAASVVNFVVVTAA 305 + +FY A+L + V+P+ G+ SPF +F AGLA AASV+N V++T+ Sbjct: 245 ILLFYALAILVMGLVLPYTNPNLVGGDVNQIAKSPFTIIFEKAGLAFAASVMNAVILTSV 304 Query: 306 ASSANSGFFSTGRMLFGLADEGHAPAAFHQLNRGGVPAPALLLTAPLLLTSIPLLYAGRS 365 S+ NSG +++ RML+ +A EG AP F ++NR GVP ALLLT + + G+ Sbjct: 305 LSAGNSGMYASTRMLWQMAKEGKAPKLFAKVNRRGVPVFALLLTTAVGAVAFLASLVGQG 364 Query: 366 VIGAFTLVTTVSSLLFMFVWAMIIISYLVYRRRHPQRHTD---SVYK---MPGG----VV 415 I + + S L W I IS+ +RR + + D VY+ P G +V Sbjct: 365 KI--YIWLLNASGLSGFIAWLGIAISHYRFRRAYVAQGRDLNHLVYRAKWFPFGPLFALV 422 Query: 416 MCWAVLVFFAFVIWTLTTETETATALAWFPL-WFVLLAVGW 455 +C V+V + +T T +++ L F+LL +G+ Sbjct: 423 LCVIVIVGQNYQAFTGNTIDWNGILVSYIGLPLFILLWLGY 463 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: 675 Number of extensions: 40 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: 484 Length adjustment: 35 Effective length of query: 521 Effective length of database: 449 Effective search space: 233929 Effective search space used: 233929 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