Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate 8501197 DvMF_1931 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= SwissProt::Q9HU16 (427 letters) >FitnessBrowser__Miya:8501197 Length = 640 Score = 370 bits (950), Expect = e-107 Identities = 190/419 (45%), Positives = 279/419 (66%), Gaps = 3/419 (0%) Query: 3 ILFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIPFF 62 +LF + +LFLL +GVPIA SLGL+ T+L + LA F + + + +LAIPFF Sbjct: 223 LLFGYFVLFLL--VGVPIAFSLGLATIATVLGAGTLPLEYLAQIAFVSIDSFPILAIPFF 280 Query: 63 LLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGSIA 122 + +G FM GG++RRL+ + VG + GG+A+A ++ CM FAA+SGS PATVAA+GSI Sbjct: 281 IAAGVFMGAGGLSRRLLALGDELVGALPGGMALATIVTCMFFAAISGSGPATVAAIGSIT 340 Query: 123 IAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLLLG 182 I MV GY + F A +V +AG +G++IPPS VVY A + SVGKLF+AG+VPG+L G Sbjct: 341 IPAMVERGYDKFFAAAVVASAGCIGVMIPPSNPFVVYGVAAQASVGKLFLAGIVPGVLCG 400 Query: 183 LILMVVIYIVARVKKLPAMPRV-SLREWLASARKALWGLLLMVIILGGIYSGAFTPTEAA 241 L LM V Y ++ K R R + + +A W LL+ VI+LGGIY G TPTEAA Sbjct: 401 LALMAVAYYISLKKGWRGEARHRDFRSVMQAMWEAKWALLVPVIVLGGIYGGIMTPTEAA 460 Query: 242 AVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQSI 301 AV+A+Y V LF+YR++ ++ES + + +++ ++A A LF +++T EQ+P I Sbjct: 461 AVSALYGMIVGLFIYREITWRRMWDCMVESAQTSSVIIVLMAMATLFGNIMTIEQVPDHI 520 Query: 302 ASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGIIM 361 A+ + + + LL++N+ LL G FME A I+I+ PI P+ ++G+DPIH G+IM Sbjct: 521 AAMILGVTSNKIAILLLINVFLLWVGTFMEALAAIVIITPILLPLVTQVGVDPIHFGVIM 580 Query: 362 VVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSLAL 420 VVN+ IG ITPPVG+NLFV S+++ + +G +RAA P+L++++ L+ +TYIPA+SL L Sbjct: 581 VVNLAIGFITPPVGVNLFVASSISKVSIGDVVRAAWPFLLVMIALLMAITYIPAISLCL 639 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: 702 Number of extensions: 41 Number of successful extensions: 4 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: 427 Length of database: 640 Length adjustment: 35 Effective length of query: 392 Effective length of database: 605 Effective search space: 237160 Effective search space used: 237160 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: 52 (24.6 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