Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate WP_029132334.1 A3GO_RS0104170 TRAP transporter large permease
Query= SwissProt::O07838 (440 letters) >NCBI__GCF_000428045.1:WP_029132334.1 Length = 428 Score = 218 bits (556), Expect = 2e-61 Identities = 137/441 (31%), Positives = 235/441 (53%), Gaps = 32/441 (7%) Query: 4 LIIFGLLIALMLTGMPISISLGLT-VLTFLFTMTQVP-IDTVALKLFTGIEKFEIMAIPF 61 L + G+L+ + L PI++++ T ++ F + + P + + + + + IP Sbjct: 9 LCMAGMLVFIALR-CPIALAMAATGLIGFTWIVAFDPALSILESGPYETLSNYGFSPIPM 67 Query: 62 FILAGNFLTHGGVAKRMINFATAMVGHWHGGLGLAGVIACALFAAVSGSSPATVVAIGSV 121 FIL G F + ++ + + A + G W GG+ LA V AC +F+A+SGSS AT ++ V Sbjct: 68 FILMGVFASKARMSTELFHAARMLFGGWRGGMALASVSACGIFSAISGSSVATAASMSRV 127 Query: 122 ILPAMVNQGFPKQFGAGVITTSGALGILIPPSIVMVMYAVATSGMVVTGPDGQPVSSASV 181 LP M G+ AG + G LGI+IPPSI +++YA+ ++ SV Sbjct: 128 ALPEMKKHGYANSLAAGTLAAGGTLGIMIPPSIALLLYAL--------------ITEQSV 173 Query: 182 GELFMAGVVPGLMLAGFLAFTTWNRARKFGYPRLEKASLRQRWTAFREAAWGL------- 234 G++FMAGV+PGL+ G L + P L + W R+ GL Sbjct: 174 GKMFMAGVIPGLL--GLLLYCATIAILVHRNPALARPGDPTTW---RQKIAGLVGFGPFF 228 Query: 235 MLIVVVIGGIYAGIFTPTEAAAMSAVYAFFISVFVYKDLTLRDVPRVLLSSANMSAMLLY 294 ++ ++IGGIY GIFTPTEAAA+ A + I++ + + L + + +SAM+ + Sbjct: 229 LVFAIIIGGIYLGIFTPTEAAAIGAFVSMVIALL--RGMRLTGFIEAVDETLKLSAMIFF 286 Query: 295 IITNAVLFSFLMAHEGIPQALGEWMVNAGLSWWMFLIIVNILLLAAGNFMEPSSIVLIMA 354 +I A +F + ++ I L E + + GL + L V +L + G M+ +++L+ Sbjct: 287 MIIGAEIFGYFLSVSRISFYLAELVGSMGLPPYAVLAAVLLLFILLGCVMDSLAMLLLTV 346 Query: 355 PILFPVAVRLGIDPVHFGIMIVVNMEVGMCHPPVGLNLYVASGIT-KMGITELTVAVWPW 413 P++FP+ V G DP+ FGI+ V+ +E+G+ PPVG+N++V + ++ I ++ V P+ Sbjct: 347 PVVFPLIVTAGFDPIWFGIVAVITVELGLITPPVGMNVFVIKSVALEIPIGQIFKGVLPF 406 Query: 414 LLTMLAFLVLVTYVPAISLAL 434 +L+ L L L+ PA++LAL Sbjct: 407 VLSDLVRLALLILFPALALAL 427 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: 548 Number of extensions: 41 Number of successful extensions: 7 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: 428 Length adjustment: 32 Effective length of query: 408 Effective length of database: 396 Effective search space: 161568 Effective search space used: 161568 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