Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate GFF2732 HP15_2676 proton/sodium-glutamate symport protein
Query= uniprot:A1S570 (437 letters) >FitnessBrowser__Marino:GFF2732 Length = 426 Score = 289 bits (739), Expect = 1e-82 Identities = 168/398 (42%), Positives = 241/398 (60%), Gaps = 13/398 (3%) Query: 14 KILIGMGAGILIGLLLRNFFGGSEWVQDYITEGFFHVIGTIFINSLKMLVVPLVFISLVC 73 K+LIGM G++ G LL G E + + G +F+ +++M+V+PLV S+V Sbjct: 8 KVLIGMFLGLITGTLLGPSVGLVEPETGTLIGNWLAFPGQLFLATIQMIVIPLVIASVVR 67 Query: 74 GTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLVQPGNASLASESMQYSAKE-- 131 G + + +L +LG + F++ TTA+A + + L+ PG +A +A E Sbjct: 68 GLAAGEDLEQLRKLGLRVTGFFVITTAMAASIGLWIGDLINPGRM-MAGLGTPVAAGENS 126 Query: 132 --------APSLADVLINIVPSNPMKALSEGNMLQIIIFAVIFGFA-ISHIGERGRRVAA 182 L LI ++P NP+ A+ EG MLQ++IF++I G A +S E+ R + Sbjct: 127 VPVASMPGVDELPKTLIGLLPGNPLDAMVEGQMLQVVIFSIIVGIALVSMAPEKSRPMLD 186 Query: 183 LFDDLNEVIMRVVTLIMQLAPYGVFALMGKLALTLGMETLESVIKYFMLVLVVLLFHGFV 242 L D L ++ M VV M+LAP VF LM +L TLG + + Y V+ LL Sbjct: 187 LLDSLQQICMTVVRWAMRLAPIAVFGLMAQLTTTLGFRAMLGMASYVATVIAGLLVL-LG 245 Query: 243 VYPTLLKLFSGLSPLMFIRKMRDVQLFAFSTASSNATLPVTMEASEHRLGADNKVASFTL 302 VY +LKL +G SP+ F++ RDV L AFST+SS A +P+++ +E +LG V+ F + Sbjct: 246 VYMLILKLLAGQSPVRFLKDTRDVLLLAFSTSSSAAVMPLSIRTAEDKLGVRPSVSQFVI 305 Query: 303 PLGATINMDGTAIMQGVATVFIAQVFGIDLTITDYAMVVMTATLASIGTAGVPGVGLVML 362 PLGATINM+GTA+ Q VAT+F+AQV+GIDL++ A+VV A ASIG+ PGVG+V+L Sbjct: 306 PLGATINMNGTALYQAVATIFLAQVYGIDLSMGSMALVVAMAVGASIGSPATPGVGIVIL 365 Query: 363 AMVLNQVGLPVEGIALILGVDRMLDMVRTAVNVTGDTV 400 AMVL VG+P GIALI+GVDR+LDM RTA+NVTGD V Sbjct: 366 AMVLQTVGIPPSGIALIMGVDRILDMCRTAINVTGDLV 403 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: 411 Number of extensions: 19 Number of successful extensions: 5 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: 426 Length adjustment: 32 Effective length of query: 405 Effective length of database: 394 Effective search space: 159570 Effective search space used: 159570 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