Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate 202250 SO3136 C4-dicarboxylate transport protein (NCBI ptt file)
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__MR1:202250 Length = 465 Score = 268 bits (685), Expect = 3e-76 Identities = 154/450 (34%), Positives = 261/450 (58%), Gaps = 38/450 (8%) Query: 12 VLILIGMPVAYALGLSALIGAWWI--DIPLQAMMIQVASGVNKFSLLAIPFFVLAGAIMA 69 + + +GMP+A ALG S+++ + D + S ++LLAIPFF+L+ A ++ Sbjct: 12 ICMFLGMPIAIALGFSSMLTILFFSNDSLASVALKLYESSSEHYTLLAIPFFILSSAFLS 71 Query: 70 EGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSVLIPEMERKG 129 GG++RR++ FA VG +RGGL++ ++MA F A+SGSS A A++GS++I M + G Sbjct: 72 TGGVARRIIDFAMDCVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIGSIVIVGMVKAG 131 Query: 130 YPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGLLLSAVMMGL 189 YP +F++ V + +L PPS ++Y AA VS+A +FMAG++PGLLL ++M + Sbjct: 132 YPEKFASGVITTSGTLGILIPPSIVMLVY--AAATEVSVAKIFMAGLVPGLLLGFLIMVV 189 Query: 190 CLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATESAAVAVVWS 249 I A+ +N P ++ + +A+ GL + I+LG I GV + TE++AVA V++ Sbjct: 190 IYIVARIKNLPSIPFPGFKKLGVSSAKAIGGLALIFIVLGSIYGGVASPTEASAVACVYA 249 Query: 250 FFVTMFIYRDY------KWRD------------------------LPKLMHRTVRT---I 276 +F+ +F YRD WR+ + K + VR + Sbjct: 250 YFIAVFGYRDIGPLKNVAWRNPNEAIPSAIARNLGHMVLGLIKTPIDKEIRHVVRDGAKV 309 Query: 277 SIVMI-LIGFAASFGYVMTLMQIPSKITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAP 335 SI+++ +I A F +V+T +IP I + + + L+ +N +L+ G M+ + Sbjct: 310 SIMLLFIIANAMLFAHVLTTERIPHIIAEYIVGMGLPAWGFLIIVNLLLLAAGNFMEPSA 369 Query: 336 LILILTPILLPVITGIGVDPVHFGMIMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVK 395 ++LI+ PIL P+ T +G+DP+H G+IM+VN+ IG++TPPVG LFV S I +I ++ Sbjct: 370 IVLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTSGITGRNIGWVIQ 429 Query: 396 ALMPFYLALFLVLMAVTYIPAISLWLPSVV 425 +++P+ + + LM +TY+P ISL+LP ++ Sbjct: 430 SVLPWLVFMLAFLMLITYVPQISLFLPELL 459 Lambda K H 0.329 0.142 0.418 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: 563 Number of extensions: 38 Number of successful extensions: 7 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: 426 Length of database: 465 Length adjustment: 32 Effective length of query: 394 Effective length of database: 433 Effective search space: 170602 Effective search space used: 170602 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 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