Align Sodium/alanine symporter AgcS; Alanine permease (characterized)
to candidate Echvi_1747 Echvi_1747 amino acid carrier protein
Query= SwissProt::Q6LX42 (453 letters) >FitnessBrowser__Cola:Echvi_1747 Length = 540 Score = 298 bits (763), Expect = 3e-85 Identities = 178/475 (37%), Positives = 258/475 (54%), Gaps = 52/475 (10%) Query: 17 PYMLVLLLGTGIFLTLRLGFMQIHTLPYALKLAFSKHQD----------------ETSEG 60 P +L+LL+ F T+ I +P ++ K+ D E G Sbjct: 61 PIVLILLVSGATFFTIYFAVPGITKMPLSINTVRGKYDDLERNYRDPENPDVIPDEAKGG 120 Query: 61 DISHFQALMTALAATIGTGNIAGVATAYVLGGPGAIFWMWVTAFFGMATKYAEAVLAIKY 120 ++SHFQAL TA++ T+G GNIAGVA A LGGPGA FWM V GM+TK+ E L +KY Sbjct: 121 EVSHFQALATAVSGTVGLGNIAGVAVAIALGGPGATFWMIVCGLLGMSTKFVECTLGVKY 180 Query: 121 RTVDDNGEMAGGPMYFLEKG----LPDHGLGKILGVAFAFFGAFAAFGIGNMVQTNSVAD 176 R ++D+G + GGPMY+L +G L LG+ LG FA A+FG GN Q+N + Sbjct: 181 RDIEDDGTVHGGPMYYLSRGLGHDLKKGRLGQFLGGLFAVLCVGASFGGGNAFQSNQASS 240 Query: 177 AVAS----NFGVDPLITGFVLAIFTAAVILGGIKSIGKATGIIVPFMAVFYILAGLVILA 232 +A+ NF + G VLA+ A VI+GGIK I T +VPFMA Y+LA L+IL Sbjct: 241 QLANLLNINFQTNGFWIGVVLAVLVAIVIIGGIKRIATITEKVVPFMAAVYVLASLIILG 300 Query: 233 MNIGYIIPAFGTIFSSAFNFSAGFGALIGTAIMWGVKRGVFSNEAGLGSAPIAAAAAKTD 292 + Y+ A G I AF AG G ++G I+ G +R FSNEAG GSA IA +A KT Sbjct: 301 AHYDYVDDAIGLIIEGAFTPMAGLGGMLGVLIV-GFQRAAFSNEAGAGSAAIAHSAVKTK 359 Query: 293 HPGRQALVSMTGTFLDTIVVCTITGLVLTIAGLKAFPGLTDL------------------ 334 P + +V++ +DT++VCT+T LV+ + GL ++ Sbjct: 360 FPASEGVVALLEPLIDTVIVCTMTALVIIFFNIDG--GLNNVESIFNYGGDGSGNVVLKE 417 Query: 335 TGAS-----LTAASFDALMPMGGLIVTIGLVFFAYSTVLGWSYYGEKCFEYLIG-TKGIR 388 TGAS LT ++D+++P ++T+ ++ FA+ST++ WSYYG + ++YL G +K Sbjct: 418 TGASIGGVELTTMAYDSVIPHFSYVLTVAIILFAFSTMISWSYYGLQSWKYLFGRSKAAD 477 Query: 389 L-YRIAFVLVAFWGATASLPLVWNIADTLNGAMAIPNLIGLLLLSGVVVSETKAF 442 L Y++ F+ GA+ +L V +D + A+ PN+IGL L V E K + Sbjct: 478 LTYKLLFIAFIVIGASTTLNAVVKFSDAMILALVFPNMIGLFFLFPKVKLELKRY 532 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: 652 Number of extensions: 43 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: 540 Length adjustment: 34 Effective length of query: 419 Effective length of database: 506 Effective search space: 212014 Effective search space used: 212014 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