Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate RR42_RS26130 RR42_RS26130 C4-dicarboxylate ABC transporter
Query= uniprot:A1S570 (437 letters) >FitnessBrowser__Cup4G11:RR42_RS26130 Length = 436 Score = 238 bits (608), Expect = 2e-67 Identities = 145/420 (34%), Positives = 239/420 (56%), Gaps = 17/420 (4%) Query: 11 LTGKILIGMGAGILIGLLLRNFFGGSEWVQDYITEGFFHVIGTIFINSLKMLVVPLVFIS 70 LT +I+I M GI+ G L F + ++ + +F ++ +F+ +KM++ PLVF + Sbjct: 6 LTTRIMIAMVLGIVTGYLCNRFVPDAAMAKEIAS--YFSIVTDVFLRLIKMIIAPLVFGT 63 Query: 71 LVCGTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLVQPGNA---SLASESMQY 127 LV G + + S +GR+G K L +++ + ++L++ + L+QPG+A L Sbjct: 64 LVAGIAGMKDASAVGRIGIKALGWFITASLLSLLLGMFFVDLLQPGHALNLPLPEIGTAT 123 Query: 128 SAKEAP-SLADVLINIVPSNPMKALSEGNMLQIIIFAVIFGFAISHI-GERGRRVAALFD 185 + K + +L D + ++ P + +A+++ +LQI++F++ FGFAI+ G+ G + A + Sbjct: 124 NLKTSTLNLKDFITHVFPKSVFEAMAQNEILQILVFSLFFGFAIASFKGKVGHHLVASIE 183 Query: 186 DLNEVIMRVVTLIMQLAPYGVFALMGKLALTLGMETLESVIKY---FMLVLVVLLFHGFV 242 +L +++RV +M+ AP GVFA + G+ L + K+ F L L+VL ++ Sbjct: 184 ELVAIMLRVTDFVMRFAPLGVFAAVAAAITVQGIGVLFTYGKFIGGFYLGLLVL----WL 239 Query: 243 VYPTLLKLFSGLSPLMFIRKMRDVQLFAFSTASSNATLPVTMEASEHRLGADNKVASFTL 302 V LF G ++ +R+ + AFSTASS A P TME E + G NKV F L Sbjct: 240 VLTAAGYLFLGGRVFTLLKLIREPTILAFSTASSEAAYPKTMEQME-KFGVPNKVTGFVL 298 Query: 303 PLGATINMDGTAIMQGVATVFIAQVFGIDLTITDYAMVVMTATLASIGTAGVPGVGLVML 362 PLG + N+DG+ + Q A +FIAQ + I++++T +++ + S G AGVP +V++ Sbjct: 299 PLGYSFNLDGSMMYQAFAALFIAQAYNIEMSLTQQITMLLVLMVTSKGIAGVPRASIVVV 358 Query: 363 AMVLNQVGLPVEGIALILGVDRMLDMVRTAVNVTGDTVATVVIAKSEGALNEAVFNDPKA 422 A L LP G+ LILG+D+ LDM RTA NV G+++AT V+AK EG L V DP A Sbjct: 359 AATLPMFNLPEAGLLLILGIDQFLDMGRTATNVIGNSIATAVVAKWEGEL--GVTQDPDA 416 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: 374 Number of extensions: 18 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: 436 Length adjustment: 32 Effective length of query: 405 Effective length of database: 404 Effective search space: 163620 Effective search space used: 163620 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