Align C4-dicarboxylate transport protein 2 (characterized)
to candidate PP_2056 PP_2056 C4-dicarboxylate transport protein
Query= SwissProt::Q9I4F5 (436 letters) >FitnessBrowser__Putida:PP_2056 Length = 435 Score = 471 bits (1211), Expect = e-137 Identities = 229/411 (55%), Positives = 308/411 (74%) Query: 8 KSLYVQVLVAIAIGIALGHWYPETAVAMKPFGDGFVKLIKMAIAPIIFCTVVTGIAGMQS 67 KSLY Q+L A+ +G+ +GH++ + AVA+KP GD F+KLIKM IAP++FCT+VTGIAGM Sbjct: 5 KSLYFQILCAVLLGVVVGHFWAQQAVALKPLGDAFIKLIKMMIAPVVFCTIVTGIAGMTD 64 Query: 68 MKSVGKTGGMALLYFEVVSTVALIIGLVVVNVVQPGAGMHVDPNTLDTSKIAAYAAAGEK 127 +S+G+ LL F ++ V+L+IGL V + +PGAGM++DP TL T+ ++ Y A+ K Sbjct: 65 KRSLGRLMSKTLLLFLGLTVVSLVIGLAAVYLFKPGAGMNIDPATLSTAGLSQYTASAAK 124 Query: 128 QSTVDFLMNVIPGTVVGAFANGDILQVLFFSVLFGYALHRLGSYGKPVFEFIERVSHVMF 187 S VDF M++IP T +GAF G++L VLF +VL G+AL +G GKPV + +E S ++F Sbjct: 125 LSVVDFFMHIIPDTFIGAFNKGEVLPVLFIAVLSGFALSSMGEKGKPVLDVLESASTMVF 184 Query: 188 NIINVIMKVAPIGAFGAMAFTIGAYGVGSLVQLGQLMLCFYITCILFVLIVLGGIARAHG 247 I +M+ APIGAFGA+AFT+G YG+ SL L +L+ YI C FVL+VLGGI RAHG Sbjct: 185 RIFGYLMRFAPIGAFGALAFTVGQYGITSLGALAKLVGTLYIACAFFVLVVLGGICRAHG 244 Query: 248 FSILRFIRYIREELLIVLGTSSSESALPRMIDKMEKLGCNKSVVGLVIPTGYSFNLDGTS 307 FS+ + +RY REE L+VLGTSS+E LPRM++K+EKLGC K VVGLV+PTGYSFNLDGT+ Sbjct: 245 FSLWKLLRYFREEFLVVLGTSSTEPVLPRMLEKLEKLGCKKGVVGLVLPTGYSFNLDGTA 304 Query: 308 IYLTMAAVFIAQATDTPMDITHQITLLLVLLIASKGAAGVTGSGFIVLAATLSAVGHLPV 367 IYL++AAVFIAQA + + + +T+L ++L++SKGAAGVTGSGF+ LA+TL+ + +P+ Sbjct: 305 IYLSLAAVFIAQACNIDLSLGQVVTMLAIMLLSSKGAAGVTGSGFVALASTLTVIHDIPL 364 Query: 368 AGLALILGIDRFMSEARALTNLVGNGVATVVVSKWCKQLDEGTLQRELAGE 418 AGLAL++G+DRFMSEARALT+L N VATVVVS D TL L GE Sbjct: 365 AGLALLIGVDRFMSEARALTSLASNAVATVVVSLSENACDRQTLHSRLNGE 415 Lambda K H 0.325 0.140 0.406 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: 577 Number of extensions: 29 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: 436 Length of database: 435 Length adjustment: 32 Effective length of query: 404 Effective length of database: 403 Effective search space: 162812 Effective search space used: 162812 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