Align SSS sodium solute transporter (characterized, see rationale)
to candidate CA265_RS06755 CA265_RS06755 sodium transporter
Query= uniprot:L0FZF3 (547 letters) >FitnessBrowser__Pedo557:CA265_RS06755 Length = 542 Score = 598 bits (1543), Expect = e-175 Identities = 308/556 (55%), Positives = 400/556 (71%), Gaps = 30/556 (5%) Query: 4 NTLDLVVFVAYCLLIITMGIVVSREKKGHVKDSKDYFLASKALPWWAVGASLIASNISAE 63 + D VF+ Y +++ G V R KK D+KDYFLA +L WWA+GAS+IASNISAE Sbjct: 5 SAFDYAVFLMYFVIVSAYGYWVYRSKKKKRTDTKDYFLAEGSLTWWAIGASIIASNISAE 64 Query: 64 QFIGMSGSGFALGLAISTYEWMAAATLLVVAIFFLPIYLKEGIYTMPQFLNRRYDGRVRT 123 FIGMSGSGFA+GLAI++YEWMAAATL++VAIFFLPIY+K IYTMPQFL+ RY+ V T Sbjct: 65 HFIGMSGSGFAMGLAIASYEWMAAATLIIVAIFFLPIYIKNKIYTMPQFLSNRYNNTVST 124 Query: 124 VMAIFWLLIYVFVNLTSVLYLGALSLETIMGVPLTYGIIGLALFAMVYSIYGGLKAVAWT 183 +MA+FWLL+YVFVNLTS+ +LGA+++ETI GVP II LA+F+ + ++ GG+K + +T Sbjct: 125 LMAVFWLLVYVFVNLTSIFFLGAIAIETITGVPFNICIIFLAIFSAIITL-GGMKVIGYT 183 Query: 184 DVVQVVFLVAGGLATTYLALSLVGD----GDVWEGIGILRKAAPSHFSMIIEKGEMMIPD 239 DV+QV LVAGGL T Y+AL LV + V + +LR A HF MI KG+ Sbjct: 184 DVIQVFVLVAGGLITCYMALKLVSEKLDAPSVLASLPLLRSEASDHFHMIFSKGDKF--- 240 Query: 240 GSGGSRDAYLDLPGLSVLIGGMWIVNLNYWGCNQYITQRALAAKSLGEAQTGMVFAGFLK 299 Y +LPG++VL+GG+WI NLNYWGCNQYI QRAL A L + G++FA FLK Sbjct: 241 --------YNELPGIAVLVGGLWINNLNYWGCNQYIVQRALGA-DLKTGRNGLIFAAFLK 291 Query: 300 LLMPLIVVIPGIAAYVIVQKGADASFIESMTDPVTGLAKSDRAYPTLLHLLPPGLKGLAF 359 LL+P+IVVIPGIAAYV+ Q+G F M D G+ K D AYP L++LLP G+KGLAF Sbjct: 292 LLIPVIVVIPGIAAYVLYQRG---YFHSEMLD-AAGVVKPDHAYPVLMNLLPAGIKGLAF 347 Query: 360 AALTAAIVSSLASMANSTSTIFTIDIYKEFFNKNVSEGKQVTIGRITAVVAFIIAAIVAP 419 AALTAAIV+SLA NS +TIFT+DIYK+F SE + V++GR + V+A +IA I+AP Sbjct: 348 AALTAAIVASLAGKCNSIATIFTLDIYKKFIKPEASETRLVSVGRWSVVIASLIAIIIAP 407 Query: 420 QLRQLDQAFQYIQEYTGFVSPGVFAIFIFGFFWKKTTSNAALTAAVLTIPLSAAFK---- 475 LR DQ +Q+IQEY GF+SPGVFAIF+ GFFWKKTTS AALTAA+LTIPLS FK Sbjct: 408 ALRSFDQVYQFIQEYVGFISPGVFAIFLLGFFWKKTTSRAALTAALLTIPLSTLFKFLPA 467 Query: 476 ----VITPNLPFIDRMGVVFLVLSVLIIAISLYEGKGKDSKKAIEVDAELFSTSTKFKVG 531 I P +PF++RM VF+++ L+I ++L + K KD+ + +E+D+ +F + F + Sbjct: 468 VTNGAIAP-IPFLNRMSWVFMIIIGLMIVVTLTDPKSKDNPQGLEIDSSMFKVTPAFTIA 526 Query: 532 AVLICGILVALYSVFW 547 +V+ICGIL ALY+VFW Sbjct: 527 SVMICGILAALYTVFW 542 Lambda K H 0.326 0.140 0.414 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: 815 Number of extensions: 39 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: 547 Length of database: 542 Length adjustment: 35 Effective length of query: 512 Effective length of database: 507 Effective search space: 259584 Effective search space used: 259584 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