Align Sodium/alanine symporter AgcS; Alanine permease (characterized)
to candidate GFF696 PGA1_c07110 putative sodium/alanine symporter
Query= SwissProt::Q6LX42 (453 letters) >FitnessBrowser__Phaeo:GFF696 Length = 514 Score = 303 bits (776), Expect = 9e-87 Identities = 173/447 (38%), Positives = 247/447 (55%), Gaps = 22/447 (4%) Query: 17 PYMLVLLLGTGIFLTLRLGFMQIHTLPYALKLAFSKHQDETSEGDISHFQALMTALAATI 76 P+++ L+ T+ G +Q P+++ L + D G++SHFQAL TAL+ T+ Sbjct: 56 PWIVAWLVIAATIFTIYFGLIQFRAFPHSISLVKGDYSDPNDAGEVSHFQALATALSGTV 115 Query: 77 GTGNIAGVATAYVLGGPGAIFWMWVTAFFGMATKYAEAVLAIKYRTVDDNGEMAGGPMYF 136 G GNIAGVA A +GGPGA FWM + GMA+K+ E L +KYR +G ++GGPMY+ Sbjct: 116 GLGNIAGVAVAVGIGGPGATFWMILAGLMGMASKFTECTLGVKYRNEYPDGTVSGGPMYY 175 Query: 137 LEKGLPDHGL--GKILGVAFAFFGAFAAFGIGNMVQTNSVADAVASNFGVDP-LITGFVL 193 + KG GL GK + V F+ F AFG GNM Q N + + G P ITG + Sbjct: 176 MTKGFAARGLPGGKFMAVLFSIFCILGAFGGGNMFQANQAHAQLTNVLGDYPGWITGVIF 235 Query: 194 AIFTAAVILGGIKSIGKATGIIVPFMAVFYILAGLVILAMNIGYIIPAFGTIFSSAFNFS 253 A AVI+GG+KSI T +VPFM V Y+L LVI+ +N I AFG IF AF Sbjct: 236 AGVVFAVIIGGLKSIASVTEKVVPFMGVLYVLTALVIILLNFDKIGWAFGQIFDGAFTGL 295 Query: 254 AGFGALIGTAIMWGVKRGVFSNEAGLGSAPIAAAAAKTDHPGRQALVSMTGTFLDTIVVC 313 G ++G A++ G KR FSNEAG+GSA IA +A +T P + VS+ F+DT+V+C Sbjct: 296 GVAGGMVG-ALIQGFKRAAFSNEAGVGSAAIAHSAVRTKEPITEGFVSLLEPFIDTVVIC 354 Query: 314 TITGLVLTIAGLKAFPGLTDL----------------TGASLTAASFDALMPMGGLIVTI 357 T+T LV+ I G T L +G +LT+A+F + I+ I Sbjct: 355 TMTALVIIITGQLVSDPETGLYVLNEAGSAIQTVDGNSGVALTSAAFSSSFGWFKYILAI 414 Query: 358 GLVFFAYSTVLGWSYYGEKCFEYLIGTKGIR--LYRIAFVLVAFWGATASLPLVWNIADT 415 ++ FA+ST++ WSYYG K + +L G ++++ F L GA ASL V + +D Sbjct: 415 AVILFAFSTMISWSYYGLKAWTFLFGESKTTELVFKVIFCLFVIIGAAASLGPVIDFSDA 474 Query: 416 LNGAMAIPNLIGLLLLSGVVVSETKAF 442 AMA+ N++ L L +V E ++ Sbjct: 475 AIFAMAVVNIVALYFLMPIVKGELNSY 501 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: 685 Number of extensions: 54 Number of successful extensions: 9 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: 514 Length adjustment: 34 Effective length of query: 419 Effective length of database: 480 Effective search space: 201120 Effective search space used: 201120 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