Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate Ac3H11_163 TRAP-type C4-dicarboxylate transport system, large permease component
Query= uniprot:I7DRS6 (467 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_163 Length = 425 Score = 298 bits (762), Expect = 3e-85 Identities = 174/459 (37%), Positives = 265/459 (57%), Gaps = 37/459 (8%) Query: 1 MDVVLLFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAI 60 M V++ +MV+ L + +AV++GL+S L + + + L SV A F L AI Sbjct: 1 MSAVMISTMVLCFALT-ISVAVSIGLASILGIQASNANMLISVKEMF--ASINKFPLAAI 57 Query: 61 PFFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIG 120 PFFILA + M TGG++RR++ F+ + VG + GGL + V CM+FAA+SGSS AT AIG Sbjct: 58 PFFILAGNLMETGGISRRLVEFAKSIVGGVQGGLPMTCVLTCMIFAAVSGSSVATTFAIG 117 Query: 121 SIVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGL 180 +I+I + + GY +AA + + LG++IPPSI M++Y + EVS+G +F+AG PGL Sbjct: 118 AILIPALIKHGYPTSYAAALQATSAELGVIIPPSIPMILYGVSAEVSIGELFIAGFGPGL 177 Query: 181 MAGLMLMVTIYVMAKVKNLPKGEWLGWGEVAASAANASVGLLLIGIILGGIYGGIFTPTE 240 + LM+ ++ K K K + G + A LL+ IILGGIYGG+FTPTE Sbjct: 178 LISGALMLFVWAYCKYKGWGKNDGDGRMPFGKATLQAGWALLMPVIILGGIYGGVFTPTE 237 Query: 241 AAAVASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHADTR 300 A+AVA YA V +YR++ K +D+ Y I Sbjct: 238 ASAVAVFYALLVGVVIYREI-------KLRDL----------------YAI--------- 265 Query: 301 HALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVILLI 360 L ++ + ++F+IANA + ++T VP I + + P +FL+ VN L + Sbjct: 266 --LRKSAISSAVIMFIIANAGLFAFLITRAGVPDAIGRWLEAVLQSPALFLLGVNAALFV 323 Query: 361 GGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTSGVA 420 G F+E S ++++AP++ P+A+ GIDP+H G+IMVVN+ +GMITPP G+NLF VA Sbjct: 324 IGMFIETSAAIIVLAPILAPVAMHFGIDPVHFGLIMVVNLALGMITPPFGVNLFAACTVA 383 Query: 421 GMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVLPNAV 459 + + +++ LPF+ V+ V L++ITY+P IS L + V Sbjct: 384 KISLDRIIKHLLPFVCVILVCLLVITYVPSISLALRDLV 422 Lambda K H 0.329 0.144 0.421 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: 557 Number of extensions: 33 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: 467 Length of database: 425 Length adjustment: 32 Effective length of query: 435 Effective length of database: 393 Effective search space: 170955 Effective search space used: 170955 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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