Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate WP_092350665.1 BLU87_RS15920 TRAP transporter large permease
Query= SwissProt::Q9HU16 (427 letters) >NCBI__GCF_900107645.1:WP_092350665.1 Length = 426 Score = 315 bits (808), Expect = 1e-90 Identities = 165/424 (38%), Positives = 259/424 (61%), Gaps = 2/424 (0%) Query: 3 ILFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIPFF 62 I F+L + GVP+A SLG+S AL +L + + + KLF + + L AIP F Sbjct: 2 IYLTFVLFIVFALFGVPVAFSLGVS-ALVFMLANGIPMALIGQKLFTGMDSFLLTAIPLF 60 Query: 63 LLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGSIA 122 +L+G M G+ LI+F+ VG IRGGLA VL M+FA ++G+ + AAVGSI Sbjct: 61 ILAGNLMNAAGLTEELIEFSKLFVGRIRGGLAYTNVLISMIFAGMTGAGVSDTAAVGSIM 120 Query: 123 IAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLLLG 182 I GM R GY + + + + T+G +IPPSI +VY + T SVG LF+AG++PG+LLG Sbjct: 121 IPGMARDGYKKDYSTAVTVISSTIGPVIPPSIPFIVYGSITGISVGALFVAGIIPGILLG 180 Query: 183 LILMVVIYIVARVKKLPAMPR-VSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEAA 241 MV I++ +R KLP + + + +R+ + + A+ L++ VIILGGI G TPTE+A Sbjct: 181 ASQMVAIFLGSRRHKLPRIEKKIPVRQKIRITKCAILALMMPVIILGGIIGGIATPTESA 240 Query: 242 AVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQSI 301 +AA Y+ + +FVYR + + KVL++SG T +M ++ A +F+++L EQ PQ++ Sbjct: 241 GIAAFYALLIGVFVYRSITPRKLIKVLIDSGVTTGAVMILLGTAAIFSYLLAAEQFPQTV 300 Query: 302 ASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGIIM 361 + V + + LL++N+ LL+ G F++ +LI+ P+F P+A +G+DPIH G+I Sbjct: 301 SEAVLSATNNKILILLLINLFLLVFGMFLDVVPALLIMTPVFLPLAQHVGVDPIHYGVIC 360 Query: 362 VVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSLALP 421 V+N+ IGL TPPVG+ LFV + + +P+ R +P+++ + L++ TY + L LP Sbjct: 361 VLNLAIGLATPPVGMCLFVGANIAKLPIEKITRPLMPFIIASFLALLVTTYWADLILFLP 420 Query: 422 NWLG 425 G Sbjct: 421 RLFG 424 Lambda K H 0.330 0.144 0.425 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: 484 Number of extensions: 27 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: 427 Length of database: 426 Length adjustment: 32 Effective length of query: 395 Effective length of database: 394 Effective search space: 155630 Effective search space used: 155630 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 (21.9 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