Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate 5208943 Shew_1444 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__PV4:5208943 Length = 465 Score = 267 bits (683), Expect = 4e-76 Identities = 155/453 (34%), Positives = 259/453 (57%), Gaps = 38/453 (8%) Query: 9 SFIVLILIGMPVAYALGLSALIGAW-WIDIPLQAMMIQVASGVNK-FSLLAIPFFVLAGA 66 S + +L+GMP+A ALG S+++ + D L ++ +++ ++ ++LLAIPFF+L+ A Sbjct: 9 SLFLCMLLGMPIAIALGFSSMLTILLFSDDSLASVALKLYESTSEHYTLLAIPFFILSSA 68 Query: 67 IMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSVLIPEME 126 ++ GG++RR++ FA VG +RGGL++ ++MA F A+SGSS A A++GS++I M Sbjct: 69 FLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIGSIVIVGMV 128 Query: 127 RKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGLLLSAVM 186 R GYP +F+ V + +L PPS ++Y AA VS A +FMAG++PGL++ ++ Sbjct: 129 RAGYPEKFAAGVITTSGTLGILIPPSIVMLVY--AAATEVSAARMFMAGLIPGLMMGLLL 186 Query: 187 MGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATESAAVAV 246 M I A+ + P R + +A+ GL +VI+LG I G+ + TE+AAVA Sbjct: 187 MLAIYIVARIKKLPSRPFPGFRPLAISSAKAMGGLALIVIVLGSIYGGIASPTEAAAVAC 246 Query: 247 VWSFFVTMFIYRD------YKWRDLPKLMHRTV--------------------------- 273 V+++F+ +F YRD WRD + + R + Sbjct: 247 VYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGFMVLAVFKTPADKEIRHVVRDG 306 Query: 274 RTISIVMI-LIGFAASFGYVMTLMQIPSKITTAFLTLSDNRYVILMCINFMLMLLGTVMD 332 +SI+++ +I A F +V+T +IP I + + + L+ +N +L+ G M+ Sbjct: 307 AKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGLPVWGFLIIVNLLLLAAGNFME 366 Query: 333 MAPLILILTPILLPVITGIGVDPVHFGMIMLVNLGIGLITPPVGAVLFVGSAIGKVSIES 392 + ++LI+ PIL P+ T +G+DP+H G+IM+VN+ IG++TPPVG LFV + I S+ Sbjct: 367 PSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGITGRSMGW 426 Query: 393 TVKALMPFYLALFLVLMAVTYIPAISLWLPSVV 425 + + +P+ L L +TYIP ISL+LP + Sbjct: 427 VIHSCIPWLALLLFFLALITYIPQISLFLPEYI 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: 545 Number of extensions: 31 Number of successful extensions: 5 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: 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