Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate HSERO_RS13470 HSERO_RS13470 C4-dicarboxylate ABC transporter
Query= SwissProt::O07838 (440 letters) >FitnessBrowser__HerbieS:HSERO_RS13470 Length = 449 Score = 260 bits (665), Expect = 5e-74 Identities = 157/452 (34%), Positives = 249/452 (55%), Gaps = 32/452 (7%) Query: 5 IIFGLL-IALMLTGMPISISLGLTVLTFL-FTMTQVPIDTVALKLFTGIEKFEIMAIPFF 62 +++G++ I +M +GMPI+ +LG+ F+ F M + +DT+ ++ I +++IP F Sbjct: 8 VLYGVVTIVVMCSGMPIAFALGVVATGFMYFFMPESSLDTITQNVYEEIASITLLSIPLF 67 Query: 63 ILAGNFLTHGGVAKRMINFATAMVGHWHGGLGLAGVIACALFAAVSGSSPATVVAIGSVI 122 IL G + K + + A + GGLG+A V ACALFAA++GSSPAT AIGS Sbjct: 68 ILKGAAIGKSPAGKDLYSAIHAWLNKVPGGLGIANVFACALFAAMAGSSPATCSAIGSAG 127 Query: 123 LPAMVNQGFPKQFGAGVITTSGALGILIPPSIVMVMYAVATSGMVVTGPDGQPVSSASVG 182 +P M +G+ F AG+I G LGIL+PPSI M++YAVA + S+G Sbjct: 128 IPEMRRRGYSPGFAAGIIAAGGTLGILLPPSITMILYAVA--------------AEQSLG 173 Query: 183 ELFMAGVVPGLMLAGFLAFTTWNRARK---------------FGYPRLEKASLRQRWTAF 227 LF+AG+ PG++L A RARK Y E +L Q+ Sbjct: 174 RLFLAGIGPGVLLVLLFAGYAVYRARKEYRLAHAVYSAGGAKSAYLDDEHFTLAQKVEML 233 Query: 228 REAAWGLMLIVVVIGGIYAGIFTPTEAAAMSAVYAFFISVFVYKDLTLRDVPRVLLSSAN 287 L+L++ V+ +Y G+ TP+E A + A+ A + VY+ R++ L S+ Sbjct: 234 PRVLPFLILLIGVMVALYGGLATPSETAGLGALLALVLIAVVYRIYKPREIAPFLSSTIK 293 Query: 288 MSAMLLYIITNAVLFSFLMAHEGIPQALGEWMVNAGLSWWMFLIIVNILLLAAGNFMEPS 347 S MLL II ++L+S++M++ I Q+ +W+V+ LS W+ L ++ +++ G F+ P Sbjct: 294 ESGMLLLIIGMSLLYSYVMSYLHISQSAAQWVVDLHLSKWLLLAVILGMVIVLGFFLPPV 353 Query: 348 SIVLIMAPILFPVAVRLGIDPVHFGIMIVVNMEVGMCHPPVGLNLYVASGIT-KMGITEL 406 SI+L+ API+ P G D + FGI++ V ME+G+ HPPVGLNL+V I + + ++ Sbjct: 354 SIILMTAPIILPPLKAAGFDLIWFGIVMTVVMEMGLIHPPVGLNLFVIKNIAPDIALGDV 413 Query: 407 TVAVWPWLLTMLAFLVLVTYVPAISLALPNLL 438 P+L M ++L+ P I+ LP+LL Sbjct: 414 IKGTIPFLALMFLAVLLLCMFPGIATLLPDLL 445 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: 596 Number of extensions: 37 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 440 Length of database: 449 Length adjustment: 32 Effective length of query: 408 Effective length of database: 417 Effective search space: 170136 Effective search space used: 170136 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