Align Sodium/alanine symporter AgcS; Alanine permease (characterized)
to candidate Echvi_2719 Echvi_2719 amino acid carrier protein
Query= SwissProt::Q6LX42 (453 letters) >FitnessBrowser__Cola:Echvi_2719 Length = 695 Score = 319 bits (818), Expect = 2e-91 Identities = 180/443 (40%), Positives = 266/443 (60%), Gaps = 18/443 (4%) Query: 17 PYMLVLLLGTGIFLTLRLGFMQIHTLPYALKLAFSKHQDETSEGDISHFQALMTALAATI 76 P++++ L+ F T ++GF+ I +A+ LA K+ + + G ISHFQA TA +AT+ Sbjct: 244 PFIVIWLVVGAAFFTFKMGFINIRGFRHAIGLATGKYDEPDAPGKISHFQAFATATSATV 303 Query: 77 GTGNIAGVATAYVLGGPGAIFWMWVTAFFGMATKYAEAVLAIKYRTVDDNGEMAGGPMYF 136 G GNIAGVA A LGGPGA FW+ + F GM++K+ E L +KYR + +G++ GGPM + Sbjct: 304 GLGNIAGVAIAISLGGPGATFWIIIAGFLGMSSKFTECTLGLKYRHIAKDGKIFGGPMNY 363 Query: 137 LEKGLPDH---GLGKILGVAFAFFGAFAAFGIGNMVQTNSVADAVASNFGVDPLITGF-- 191 L+ GL LGK+L FA F +FG GNM Q N +A+ F P++ GF Sbjct: 364 LKHGLERRNMKNLGKVLAAVFAIFCVAFSFGGGNMFQANQSYKILATQF---PVLEGFGF 420 Query: 192 ----VLAIFTAAVILGGIKSIGKATGIIVPFMAVFYILAGLVILAMNIGYIIPAFGTIFS 247 +LAI VI+GGI+SI K T IVPFMA YI LV++ +NIG I AF I+ Sbjct: 421 WVGVILAILVGVVIIGGIESIAKVTEKIVPFMAGLYIFGALVVIFVNIGNIGQAFNAIWD 480 Query: 248 SAFNFSAGFGALIGTAIMWGVKRGVFSNEAGLGSAPIAAAAAKTDHPGRQALVSMTGTFL 307 AFN +A G IG ++ G +RGVFSNEAG GSA IA +A KT++P + V + F+ Sbjct: 481 GAFNATAMKGGFIGVLVV-GFQRGVFSNEAGTGSAAIAHSAVKTNNPPSEGFVGLLEPFV 539 Query: 308 DTIVVCTITGLVLTIAGLKAFPGLTDLTGASLTAASFDALMPMGGLIVTIGLVFFAYSTV 367 DTIVVCT+T LV+ G G + G LT+ +F +++ ++ I ++ FA+S++ Sbjct: 540 DTIVVCTLTALVIIFTGKHEAQG---MGGVELTSQAFASVISWFPYLLAIAVLLFAFSSM 596 Query: 368 LGWSYYGEKCFEYLIG--TKGIRLYRIAFVLVAFWGATASLPLVWNIADTLNGAMAIPNL 425 + WSYYG + + YL G + Y++ FV+ GA+ SL V + +D + +M+ PN+ Sbjct: 597 VSWSYYGLRSWTYLFGKSKRSELAYKLVFVVFVVIGASISLGAVLDFSDMMILSMSFPNI 656 Query: 426 IGLLLLSGVVVSETKAFNEIRKN 448 IGL ++SG V ++ ++ + KN Sbjct: 657 IGLYIMSGEVRNDMNSYLKKLKN 679 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: 807 Number of extensions: 50 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: 695 Length adjustment: 36 Effective length of query: 417 Effective length of database: 659 Effective search space: 274803 Effective search space used: 274803 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: 53 (25.0 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