Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate 7024207 Shewana3_1414 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__ANA3:7024207 Length = 465 Score = 264 bits (675), Expect = 4e-75 Identities = 152/453 (33%), Positives = 259/453 (57%), Gaps = 38/453 (8%) Query: 6 LLGSFIVLILIGMPVAYALGLSALIGAWWI--DIPLQAMMIQVASGVNKFSLLAIPFFVL 63 L + +V + +GMP+A ALG S+++ + D + S ++LLAIPFF+L Sbjct: 6 LFTALLVCMFLGMPIAIALGFSSMLTILFFSNDSLASVALKLYESSSEHYTLLAIPFFIL 65 Query: 64 AGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSVLIP 123 + A ++ GG++RR++ FA +G +RGGL++ ++MA F A+SGSS A A++GS++I Sbjct: 66 SSAFLSTGGVARRIIDFAMDSIGHIRGGLAMASVMACMLFAAVSGSSPATVAAIGSIVIV 125 Query: 124 EMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGLLLS 183 M + GYP +F+ V + +L PPS ++Y AA VS A +FMAG++PGL++ Sbjct: 126 GMVKAGYPEKFAAGVITTSGTLGILIPPSIVMLVY--AAATEVSAARMFMAGLIPGLMMG 183 Query: 184 AVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATESAA 243 ++M + I A+ +N P ++ + +AL GL ++I+LG I GV + TE++A Sbjct: 184 FLLMIVIYIVARFKNLPSRPFPGFKQLGISSAKALGGLALIIIVLGSIYGGVASPTEASA 243 Query: 244 VAVVWSFFVTMFIYRDY------KWRD------------------------LPKLMHRTV 273 VA ++++F+ +F YRD WR+ + K + V Sbjct: 244 VACMYAYFIAVFGYRDIGPLKNVAWRNPNEPIPSAIVRNLGHMALGLIKTPIDKEIRHVV 303 Query: 274 RT---ISIVMI-LIGFAASFGYVMTLMQIPSKITTAFLTLSDNRYVILMCINFMLMLLGT 329 R +SI+++ +I A F +V+T +IP I + + + L+ +N +L+ G Sbjct: 304 RDGAKVSIMLLFIIANAMLFAHVLTTERIPHIIAEHIVGMGLPAWGFLIIVNLLLLAAGN 363 Query: 330 VMDMAPLILILTPILLPVITGIGVDPVHFGMIMLVNLGIGLITPPVGAVLFVGSAIGKVS 389 M+ + ++LI+ PIL P+ T +G+DP+H G+IM+VN+ IG++TPPVG LFV + I S Sbjct: 364 FMEPSAIVLIMAPILFPIATHLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGITGRS 423 Query: 390 IESTVKALMPFYLALFLVLMAVTYIPAISLWLP 422 I +++++P+ + L +TY+P ISL+LP Sbjct: 424 IGWVIQSVLPWLALMLAFLALITYVPQISLFLP 456 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: 535 Number of extensions: 30 Number of successful extensions: 5 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