Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate 3609368 Dshi_2753 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= SwissProt::Q9HU16 (427 letters) >FitnessBrowser__Dino:3609368 Length = 429 Score = 317 bits (813), Expect = 3e-91 Identities = 169/429 (39%), Positives = 268/429 (62%), Gaps = 5/429 (1%) Query: 3 ILFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSVRSLAI---KLFETSEHYTLLAI 59 +L FL LFLL F+ + + V GL A +LL+ R + + ++ + + L+AI Sbjct: 1 MLIWFLPLFLL-FLMIGLPVFFGLLAAPGLLLWLNGQERDITLLYRNVYNGMDSFPLMAI 59 Query: 60 PFFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVG 119 PFF+L+G M GG+ RL++FA A +GH RGGLA +L+ MLFA LSGS+ A +A+G Sbjct: 60 PFFMLAGELMNRGGITLRLVEFAQALMGHFRGGLAHVNILSSMLFAGLSGSAVADTSALG 119 Query: 120 SIAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGL 179 S+ I M + GY + F A I + +G +IPPS +M++YA SV LF+AG+VPG+ Sbjct: 120 SMLIPAMEKQGYTRRFAAAITAASSVIGPIIPPSGIMIIYAYVMGESVAALFLAGIVPGI 179 Query: 180 LLGLILMVVIYIVARVKKLP-AMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPT 238 L+G+ LM V+ ++A P A + + + ++ KA + L+ VIILGGI +G FTPT Sbjct: 180 LVGVGLMGVVKLMADKYDFPVASAKTTWGQRGQASLKAFFPLMTPVIILGGILAGVFTPT 239 Query: 239 EAAAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIP 298 EAAAVA Y+ + FV R +++S+ P +L +G + +++ ++ AM F V++ P Sbjct: 240 EAAAVAVAYALIIGFFVMRTLKVSDLPDILGRAGITSAVVLLLVGAAMAFKTVVSLSYAP 299 Query: 299 QSIASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLG 358 Q +A ++ L +P + LL++N++L + G F++ I+IL PI PI ++LG+DPIH Sbjct: 300 QIMADFMLSLSENPLILLLLINLLLFVVGMFLDAGPAIIILGPILGPIFVDLGVDPIHFA 359 Query: 359 IIMVVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSL 418 IIM VN+ +GL TPP+GL LFV S+V+G + +A LP+L + ++ + ++TY PA+S+ Sbjct: 360 IIMSVNLTVGLATPPMGLVLFVASSVSGERVERIAKAILPFLAVEILVIFLITYFPAISM 419 Query: 419 ALPNWLGMS 427 +P G + Sbjct: 420 TIPRLTGFA 428 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: 476 Number of extensions: 23 Number of successful extensions: 2 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: 429 Length adjustment: 32 Effective length of query: 395 Effective length of database: 397 Effective search space: 156815 Effective search space used: 156815 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 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