Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate AZOBR_RS26625 AZOBR_RS26625 dehydroascorbate transporter
Query= SwissProt::Q9HU16 (427 letters) >FitnessBrowser__azobra:AZOBR_RS26625 Length = 427 Score = 298 bits (763), Expect = 2e-85 Identities = 155/423 (36%), Positives = 257/423 (60%) Query: 1 MTILFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIP 60 +TI+ L M +G+PIA +L +SG + + + +++ + + LLA+P Sbjct: 1 VTIVIFVGSLLGAMALGLPIAFALIVSGLALMAFMGMLDPQIVVQSMWDGANSFPLLAVP 60 Query: 61 FFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGS 120 FF+L+G FM GG++RR+I A A VGH+RGGL AV A +L A+LSGS+ A AA+ S Sbjct: 61 FFMLAGEFMNAGGMSRRIIAMAMAWVGHLRGGLGFVAVFAAILMASLSGSAVADTAALAS 120 Query: 121 IAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLL 180 I + M ++GY G++ G + +IPPSI M++Y A + S+ KLF+AG+VPG++ Sbjct: 121 ILLPMMRQAGYDIHRSGGLIAAGGIIAPVIPPSIGMILYGVAGQVSITKLFLAGIVPGIM 180 Query: 181 LGLILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEA 240 +G+ L++ + +AR + L P+V LRE L A W +LL V+I+GG+ +G FTPTEA Sbjct: 181 MGVALLITWWWLARREILTTPPKVPLRERLRLTADAFWAMLLPVVIIGGLKTGVFTPTEA 240 Query: 241 AAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQS 300 A VAAVY+ FV L +YR++R+++ ++L + K T ++MF++A A + A ++T IP Sbjct: 241 AVVAAVYAMFVGLVIYRELRIADLYGLMLSAAKTTAVVMFLVAAAGISAWLITASNIPAQ 300 Query: 301 IASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGII 360 +A + + + + +L + +++LI G ++ + IL++ P+ PI + GIDP++ G++ Sbjct: 301 LADLLAPVMDNRLLLMLALMVIVLIVGTALDFAPTILLMVPVLMPIIKQAGIDPVYFGVL 360 Query: 361 MVVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSLAL 420 ++N IGLITPPVG L V V M + ++ P+L+ L ++ P + +A Sbjct: 361 FIMNNAIGLITPPVGTVLNVVCGVGRMSMSNLMKGVGPFLLAQTAVLFLLVLFPELVMAP 420 Query: 421 PNW 423 W Sbjct: 421 LAW 423 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: 488 Number of extensions: 25 Number of successful extensions: 1 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: 427 Length adjustment: 32 Effective length of query: 395 Effective length of database: 395 Effective search space: 156025 Effective search space used: 156025 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