Align Sodium/alanine symporter AgcS; Alanine permease (characterized)
to candidate 206150 DVU0724 sodium/alanine symporter family protein
Query= SwissProt::Q6LX42 (453 letters) >MicrobesOnline__882:206150 Length = 468 Score = 462 bits (1190), Expect = e-135 Identities = 244/451 (54%), Positives = 310/451 (68%), Gaps = 14/451 (3%) Query: 1 MDFVSLVNTVNSFVWGPYMLVLLLGTGIFLTLRLGFMQIHTLPYALKLAFSKHQDETSEG 60 M + L +VN+FVWGP +L LL+GTGI+LT+RLG +Q+ LP AL+ F + + EG Sbjct: 1 MTTLQLFESVNAFVWGPPLLALLVGTGIYLTIRLGLLQVVRLPLALRYVFGRDDEHHEEG 60 Query: 61 DISHFQALMTALAATIGTGNIAGVATAYVLGGPGAIFWMWVTAFFGMATKYAEAVLAIKY 120 D+S F AL TALAATIGTGNI GVATA GGPGA+FWMWV AFFGMATKYAE +LA+KY Sbjct: 61 DVSSFAALCTALAATIGTGNIVGVATAVAAGGPGALFWMWVAAFFGMATKYAEGLLAVKY 120 Query: 121 RTVDDNGEMAGGPMYFLEKGLPDHGLGKILGVAFAFFGAFAA-FGIGNMVQTNSVADAVA 179 R D NG+M+GGPMY+LE+GL ++L AFA G A FGIG Q N++ DA + Sbjct: 121 RVTDANGQMSGGPMYYLERGLG----SRMLARAFALCGILVAFFGIGTFAQVNAIKDAAS 176 Query: 180 SNFGVDPLITGFVLAIFTAAVILGGIKSIGKATGIIVPFMAVFYILAGLVILAMNIGYII 239 + G+ PL T VL A V LGG++SI + +VPFMAVFYI+A +L M++ I Sbjct: 177 LSLGIPPLATAVVLTTTVALVTLGGLRSIARVAEKVVPFMAVFYIIASCAVLVMHLDRIP 236 Query: 240 PAFGTIFSSAFNFSAGFGALIG----TAIMWGVKRGVFSNEAGLGSAPIAAAAAKTDHPG 295 A I SAFN A G G TA+ GV RGVFSNE+GLGSAPIAAAAA+T Sbjct: 237 DAVMVILHSAFNPQAALGGAAGMTVLTAMRAGVARGVFSNESGLGSAPIAAAAARTKSCV 296 Query: 296 RQALVSMTGTFLDTIVVCTITGLVLTIAGLKAFPGLTDLTGASLTAASFDALM--PMGGL 353 RQ L+SMTGTF DTIV+CT+TGLVL + G+ P L GA++T A+F A + +G Sbjct: 297 RQGLISMTGTFFDTIVICTMTGLVLVVTGVWNDP---QLAGAAMTNAAFAAGLESSLGQY 353 Query: 354 IVTIGLVFFAYSTVLGWSYYGEKCFEYLIGTKGIRLYRIAFVLVAFWGATASLPLVWNIA 413 T+GL+ FA++T+LGW+YYGE+C EYL G +GI YR+ F+ + GA L L+W +A Sbjct: 354 AATLGLILFAFTTILGWNYYGERCTEYLFGVRGILPYRLVFIGLVAAGAFVHLELIWVLA 413 Query: 414 DTLNGAMAIPNLIGLLLLSGVVVSETKAFNE 444 D +NG MAIPNLIGLL LSGV+++ET+AF E Sbjct: 414 DIVNGLMAIPNLIGLLGLSGVIIAETRAFFE 444 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: 39 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: 453 Length of database: 468 Length adjustment: 33 Effective length of query: 420 Effective length of database: 435 Effective search space: 182700 Effective search space used: 182700 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: 51 (24.3 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