Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate 5209774 Shew_2227 sodium:dicarboxylate symporter (RefSeq)
Query= uniprot:A1S570 (437 letters) >FitnessBrowser__PV4:5209774 Length = 439 Score = 703 bits (1815), Expect = 0.0 Identities = 359/434 (82%), Positives = 402/434 (92%) Query: 1 MAAAQSSKIGLTGKILIGMGAGILIGLLLRNFFGGSEWVQDYITEGFFHVIGTIFINSLK 60 MA Q+ K+GLTGKILIGM GIL GLLLR+FF GSE++++YIT G +V+G+IFI+SL+ Sbjct: 1 MAGTQNKKLGLTGKILIGMAGGILTGLLLRSFFPGSEFIEEYITNGLLNVVGSIFISSLQ 60 Query: 61 MLVVPLVFISLVCGTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLVQPGNASL 120 MLVVPLVFISLVCGTCSLS+PS LGRLGGKT+AFYLFTTAIAL +AI A+LV PGNASL Sbjct: 61 MLVVPLVFISLVCGTCSLSDPSSLGRLGGKTIAFYLFTTAIALSMAILVALLVHPGNASL 120 Query: 121 ASESMQYSAKEAPSLADVLINIVPSNPMKALSEGNMLQIIIFAVIFGFAISHIGERGRRV 180 A+E+MQYS KEAPSL+DVLIN+VP NP++A++EGNMLQIIIFAVIFGFAISHIGERG+RV Sbjct: 121 AAENMQYSVKEAPSLSDVLINLVPRNPIQAMTEGNMLQIIIFAVIFGFAISHIGERGKRV 180 Query: 181 AALFDDLNEVIMRVVTLIMQLAPYGVFALMGKLALTLGMETLESVIKYFMLVLVVLLFHG 240 +ALF+DLNEVIMRVVTLIMQLAPYG+FALMGKLALTLG+ET ESV+KYFM+VL VLL H Sbjct: 181 SALFNDLNEVIMRVVTLIMQLAPYGIFALMGKLALTLGLETFESVVKYFMVVLAVLLVHA 240 Query: 241 FVVYPTLLKLFSGLSPLMFIRKMRDVQLFAFSTASSNATLPVTMEASEHRLGADNKVASF 300 FV YP LLKLFSGLSP FIRKMRDVQLFAFSTASSNATLPVT+E SEHRLG DNKVASF Sbjct: 241 FVSYPVLLKLFSGLSPFTFIRKMRDVQLFAFSTASSNATLPVTLETSEHRLGVDNKVASF 300 Query: 301 TLPLGATINMDGTAIMQGVATVFIAQVFGIDLTITDYAMVVMTATLASIGTAGVPGVGLV 360 TLPLGATINMDGTAIMQGVATVFIAQVFGIDLTITDYAMVV+TATLASIGTAGVPGVGL+ Sbjct: 301 TLPLGATINMDGTAIMQGVATVFIAQVFGIDLTITDYAMVVVTATLASIGTAGVPGVGLI 360 Query: 361 MLAMVLNQVGLPVEGIALILGVDRMLDMVRTAVNVTGDTVATVVIAKSEGALNEAVFNDP 420 MLAMVLNQVGLPVEGIALI+GVDR+LDMVRTAVNVTGD+VATV+IAKSE A N+A F+DP Sbjct: 361 MLAMVLNQVGLPVEGIALIMGVDRLLDMVRTAVNVTGDSVATVIIAKSENAFNQATFDDP 420 Query: 421 KAGKTAGSFDAEVH 434 +AGKTAGSF +V+ Sbjct: 421 QAGKTAGSFVDQVN 434 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: 580 Number of extensions: 16 Number of successful extensions: 1 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: 439 Length adjustment: 32 Effective length of query: 405 Effective length of database: 407 Effective search space: 164835 Effective search space used: 164835 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