Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate PfGW456L13_970 L-cystine uptake protein TcyP
Query= uniprot:A1S570 (437 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_970 Length = 463 Score = 202 bits (515), Expect = 1e-56 Identities = 140/429 (32%), Positives = 226/429 (52%), Gaps = 27/429 (6%) Query: 1 MAAAQSSKIGLTGKILIGMGAGILIGLLLRNFFGGSEWVQDYITEGFFHVIGTIFINSLK 60 +A + + L K+L+ + G+ G+ L +G V + G+F ++G ++ L+ Sbjct: 19 LAQTRHTTWSLAKKVLLALVLGVAFGVTLHTVYGAGNPVLK-ASIGWFDLVGNGYVQLLQ 77 Query: 61 MLVVPLVFISLVCGTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLV------- 113 M+V+PLVF S++ L S LG++ T+ LFTTAIA ++ I L Sbjct: 78 MIVIPLVFASILSAVARLHNASSLGKISFLTIGTLLFTTAIAALIGIGLTNLFGLTAEGL 137 Query: 114 ---QPGNASLASESMQYSAKEAP-SLADVLINIVPSNPMKALSEG---NMLQIIIFAVIF 166 A L + Y+ K A ++ +L++ +P NP L+ +++ ++IFA Sbjct: 138 VAGTQEMARLQTIQTDYAGKVADLNVPQLLLSFIPQNPFADLARAKPTSIISVVIFAAFL 197 Query: 167 GFAISHI----GERGRRVAALFDDLNEVIMRVVTLIMQLAPYGVFALMGKLALTLGMETL 222 G A + E+G++V D L +MR+V L+M+L PYGV ALM K+ + L Sbjct: 198 GVAALQLLKDDAEKGQKVINAIDTLQAWVMRLVRLVMKLTPYGVLALMTKV---VAGSNL 254 Query: 223 ESVIKYFMLVLVVLLFHG--FVVYPTLLKLFSGLSPLMFIRKMRDVQLFAFSTASSNATL 280 + +IK V+V + G FVV+ L+ +G++PL F RK+ V FAF++ SS AT+ Sbjct: 255 QDIIKLGSFVVVSYIGLGLMFVVHGVLVSA-AGINPLRFFRKIWPVLTFAFTSRSSAATI 313 Query: 281 PVTMEASEHRLGADNKVASFTLPLGATINMDGTA-IMQGVATVFIAQVFGID-LTITDYA 338 P+++EA RLG +ASF GATI +G A + + V +A GI+ L A Sbjct: 314 PLSIEAQTSRLGIPQSIASFAASFGATIGQNGCAGLYPAMLAVMVAPTVGINPLDPLWIA 373 Query: 339 MVVMTATLASIGTAGVPGVGLVMLAMVLNQVGLPVEGIALILGVDRMLDMVRTAVNVTGD 398 +V TL+S G AGV G +VL +GLPV +AL++ V+ ++DM RTA+NV+G Sbjct: 374 TLVAIVTLSSAGVAGVGGGATFAALIVLPAMGLPVSLVALLISVEPLIDMGRTALNVSGS 433 Query: 399 TVATVVIAK 407 A + ++ Sbjct: 434 ITAGAITSQ 442 Lambda K H 0.325 0.139 0.388 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: 406 Number of extensions: 27 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: 437 Length of database: 463 Length adjustment: 33 Effective length of query: 404 Effective length of database: 430 Effective search space: 173720 Effective search space used: 173720 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 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