Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate WP_092346873.1 BLU87_RS08690 TRAP transporter large permease
Query= uniprot:I7DRS6 (467 letters) >NCBI__GCF_900107645.1:WP_092346873.1 Length = 428 Score = 275 bits (702), Expect = 3e-78 Identities = 160/457 (35%), Positives = 258/457 (56%), Gaps = 37/457 (8%) Query: 1 MDVVLLFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAI 60 M+ + + + I L +G+PIA LG++ L ++++ D L + ++ G F LA+ Sbjct: 1 METLSIVGVFILTLFLGMPIAFVLGITG-LVMVLFIDVPLVVLPNRMWSQL-GTFPFLAV 58 Query: 61 PFFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIG 120 PFFILA M G+ +R++ F+ VG + GGL + A MLFA ++GS+ A+G Sbjct: 59 PFFILAGEIMNEAGITQRLVSFANLLVGRIRGGLGQVNIIASMLFAGITGSAIGDTAALG 118 Query: 121 SIVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGL 180 SI+I M + GY K+F+ V ++ +G +IPPS++M++ A E S+G +F+AG +PG+ Sbjct: 119 SIMIPAMEKEGYDKDFSVAVTASSSIIGPIIPPSLLMIILGVAAEQSIGTLFVAGYVPGI 178 Query: 181 MAGLMLMVTIYVMAKVKNLP-KGEWLGWGEVAASAANASVGLLLIGIILGGIYGGIFTPT 239 + G+ LM+ Y ++ +N + E + + A + LL+ II+ GI GIFT T Sbjct: 179 LIGVSLMILTYFISIKRNYTFRAERTSFRQGLIIFRKALIPLLMPIIIIVGILAGIFTAT 238 Query: 240 EAAAVASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHADT 299 EAAAVA VYA FV FV + + L LP + Sbjct: 239 EAAAVACVYALFVGLFVTKTLK--------------LKRLPDLF---------------I 269 Query: 300 RHALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVILL 359 R AL LT +L +++ + I +T Q+ ++++ A+ P + L+++N++LL Sbjct: 270 RSAL-----LTASLHLIVSMSGISGFAVTVLQLAEKMSAAVTQFSTNPFVILLLLNIVLL 324 Query: 360 IGGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTSGV 419 I G FMEP+ ++I+ P++FP+ LGI P+H GIIM++N+ IG+ TPP+GL LF S V Sbjct: 325 IIGMFMEPTVSIIILVPILFPMIEALGIHPVHFGIIMLMNLTIGVATPPLGLVLFTASSV 384 Query: 420 AGMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVLP 456 +P+ VV A PFL + FV L++ITYIP ++ +P Sbjct: 385 GKIPVERVVMAIWPFLLIEFVVLLLITYIPALTLTIP 421 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: 610 Number of extensions: 35 Number of successful extensions: 3 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: 467 Length of database: 428 Length adjustment: 33 Effective length of query: 434 Effective length of database: 395 Effective search space: 171430 Effective search space used: 171430 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