Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate WP_007474714.1 CMTB2_RS05790 C4-dicarboxylate ABC transporter permease
Query= SwissProt::O07838 (440 letters) >NCBI__GCF_000170735.1:WP_007474714.1 Length = 427 Score = 434 bits (1117), Expect = e-126 Identities = 216/440 (49%), Positives = 307/440 (69%), Gaps = 17/440 (3%) Query: 1 MSALIIFGLLIALMLTGMPISISLGLTVL--TFLFTMTQVPIDTVALKLFTGIEKFEIMA 58 M +FGL +L +P+++SLGL+ L ++F + + ID ++ LF+ ++K+ +MA Sbjct: 1 MIVATLFGLFFLFLLLSVPVAVSLGLSTLITAYIFEGSDLLID-LSSNLFSQLDKYALMA 59 Query: 59 IPFFILAGNFLTHGGVAKRMINFATAMVGHWHGGLGLAGVIACALFAAVSGSSPATVVAI 118 IP FILAG+ L+ GG AKR+I FA A VGH GGL +A + A +FAAVSGSSPATV AI Sbjct: 60 IPMFILAGSLLSKGGSAKRIIEFAKAFVGHLPGGLPIAAIFASIIFAAVSGSSPATVAAI 119 Query: 119 GSVILPAMVNQGFPKQFGAGVITTSGALGILIPPSIVMVMYAVATSGMVVTGPDGQPVSS 178 GS++ A+++ G+PK + G ITT+G+LGILIPPSIVM++Y V + Sbjct: 120 GSIMFGAILSAGYPKTYAIGTITTAGSLGILIPPSIVMIIYGVT--------------AE 165 Query: 179 ASVGELFMAGVVPGLMLAGFLAFTTWNRARKFGYPRLEKASLRQRWTAFREAAWGLMLIV 238 S+G+LFMAGV+PG+++ L + A++ G+ + AS ++RW F+EA W LM IV Sbjct: 166 QSIGKLFMAGVIPGILIGSMLMLVAYFGAKRLGFKTTKPASWKERWQKFKEAFWALMTIV 225 Query: 239 VVIGGIYAGIFTPTEAAAMSAVYAFFISVFVYKDLTLRDVPRVLLSSANMSAMLLYIITN 298 ++IGGIY GIFTPTEAAA+SA++A F+S+ +YKD+ ++D+ + SA +S M+L+II N Sbjct: 226 IIIGGIYGGIFTPTEAAAVSAIWALFVSLVIYKDIQIKDLGNIFFESAKVSGMILFIIAN 285 Query: 299 AVLFSFLMAHEGIPQALGEWMVNAGLSWWMFLIIVNILLLAAGNFMEPSSIVLIMAPILF 358 A +F++ + E IPQ L + +V L+ FLI VNI+LL AGNFMEPSSI++IM P+L Sbjct: 286 ASMFAYFLTLENIPQMLTDLVVQMNLNKVTFLIAVNIILLIAGNFMEPSSIIMIMVPLLL 345 Query: 359 PVAVRLGIDPVHFGIMIVVNMEVGMCHPPVGLNLYVASGITKMGITELTVAVWPWLLTML 418 P+A LGIDP+HFG++I +NME+GM PPVGLNL+VASGIT I E+ +V PW + ML Sbjct: 346 PIAKMLGIDPIHFGVIITINMELGMLTPPVGLNLFVASGITGESIKEVVKSVLPWFIVML 405 Query: 419 AFLVLVTYVPAISLALPNLL 438 L+L+TY+P ISL LP + Sbjct: 406 FGLILITYIPKISLWLPKTM 425 Lambda K H 0.329 0.142 0.431 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: 630 Number of extensions: 33 Number of successful extensions: 3 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: 440 Length of database: 427 Length adjustment: 32 Effective length of query: 408 Effective length of database: 395 Effective search space: 161160 Effective search space used: 161160 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 24 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