Align Sodium/alanine symporter AgcS; Alanine permease (characterized)
to candidate 3608408 Dshi_1808 amino acid carrier protein (RefSeq)
Query= SwissProt::Q6LX42 (453 letters) >FitnessBrowser__Dino:3608408 Length = 512 Score = 309 bits (791), Expect = 2e-88 Identities = 185/451 (41%), Positives = 258/451 (57%), Gaps = 25/451 (5%) Query: 12 SFVWGPYMLVLLLGTGIFLTLRLGFMQIHTLPYALKLAFSKHQDETSEGDISHFQALMTA 71 SF W +L L++ IF T+ GF+Q+ +++KL + D G++SHFQAL TA Sbjct: 53 SFPW--IVLWLVVAASIF-TVYFGFIQLRGFVHSIKLVKGDYADPDDAGEVSHFQALATA 109 Query: 72 LAATIGTGNIAGVATAYVLGGPGAIFWMWVTAFFGMATKYAEAVLAIKYRTVDDNGEMAG 131 L+ T+G GNIAGVA A +GGPGA FWM GMA+K+ E L +KYR +G ++G Sbjct: 110 LSGTVGLGNIAGVAVAVGIGGPGATFWMIFAGLLGMASKFTECTLGVKYRNEYPDGTVSG 169 Query: 132 GPMYFLEKGLPDHGL--GKILGVAFAFFGAFAAFGIGNMVQTNSVADAVASNFGVDP-LI 188 GPMY++ KG + G+ GK + V F+ F A G GNM Q N ++ G P I Sbjct: 170 GPMYYISKGFAEKGMPGGKFMAVLFSIFCILGALGGGNMFQANQAHAQISGIVGDYPGWI 229 Query: 189 TGFVLAIFTAAVILGGIKSIGKATGIIVPFMAVFYILAGLVILAMNIGYIIPAFGTIFSS 248 TG + A AVI+GGIKSI K T +VPFM + Y+ A LVIL +NI I AFG IF Sbjct: 230 TGIIFAAVVFAVIVGGIKSIAKVTEKVVPFMGILYVAAALVILLVNIDQIGWAFGQIFEG 289 Query: 249 AFNFSAGFGALIGTAIMWGVKRGVFSNEAGLGSAPIAAAAAKTDHPGRQALVSMTGTFLD 308 AF G +G A++ G KR FSNEAG+GSA IA +A KT P + VS+ F+D Sbjct: 290 AFTGLGVAGGFVG-ALIQGFKRAAFSNEAGVGSAAIAHSAVKTKEPVTEGYVSLLEPFID 348 Query: 309 TIVVCTITGLVLTIAGLKAFPGLTDL--------------TGASLTAASFDALMPMGGLI 354 T+V+CT+T LV+TI+G T L +G +LT+A+F + Sbjct: 349 TVVICTMTALVITISGQLMINPDTGLYMVENGAIMTVDGNSGVALTSAAFATGFSWFPYV 408 Query: 355 VTIGLVFFAYSTVLGWSYYGEKCFEYLIG---TKGIRLYRIAFVLVAFWGATASLPLVWN 411 + I +V FA+ST++ WSYYG K + YL G TK + ++++ F + GA ASL V + Sbjct: 409 LAIAVVLFAFSTMISWSYYGLKAWTYLFGEGRTKEL-VFKVIFCVFVVIGAAASLGPVID 467 Query: 412 IADTLNGAMAIPNLIGLLLLSGVVVSETKAF 442 +D AMA+ N+ L +L VV +E ++ Sbjct: 468 FSDAAIFAMAVVNIAALYVLMPVVKAELASY 498 Lambda K H 0.326 0.141 0.424 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: 661 Number of extensions: 47 Number of successful extensions: 7 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: 453 Length of database: 512 Length adjustment: 34 Effective length of query: 419 Effective length of database: 478 Effective search space: 200282 Effective search space used: 200282 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 (21.6 bits) S2: 52 (24.6 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