Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate HSERO_RS04250 HSERO_RS04250 C4-dicarboxylate ABC transporter permease
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__HerbieS:HSERO_RS04250 Length = 426 Score = 320 bits (821), Expect = 4e-92 Identities = 158/426 (37%), Positives = 265/426 (62%), Gaps = 3/426 (0%) Query: 1 MEAFILLGSFIVLILIGMPVAYALGLSALIGAWWI-DIPLQAMMIQVASGVNKFSLLAIP 59 M A I+ L+L GMP++ +LGL+ L + + ++P+Q++ +++ +G+ KF ++AIP Sbjct: 1 MNALIIFVLLFALMLTGMPISISLGLTVLTFLFTMTEVPIQSVALKLFTGIEKFEIMAIP 60 Query: 60 FFVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGS 119 FF+LAG + GG++RR++ FA +VG GGL+L ++A F A+SGSS A ++GS Sbjct: 61 FFILAGNFLTHGGVARRMINFATSMVGHWHGGLALAGVLACALFAAVSGSSPATVVAIGS 120 Query: 120 VLIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPG 179 +++P M ++G+P F V + +L PPS V+YS++ S+ LFMAG++PG Sbjct: 121 IILPAMVKQGFPNRFGAGVITTSGALGILIPPSIVMVMYSVSTN--TSVGKLFMAGVVPG 178 Query: 180 LLLSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTAT 239 LLL+ ++ A+K NYP+ + E ++ WGL +VI++GGI +GVFT T Sbjct: 179 LLLAFLLGVTTWFLARKNNYPRLKKATWAERAAAFRKSGWGLFLIVIVMGGIYTGVFTPT 238 Query: 240 ESAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIP 299 E+AA+A V++FF+ +F+Y+D + +PK++ + ++++ +I A F +++T IP Sbjct: 239 EAAAMAAVYAFFIAVFVYKDLTLKQVPKVLLDSASMSAMLLYIITNAVLFSFLVTSENIP 298 Query: 300 SKITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFG 359 + L+ +N +L+L G VM+ + ++LIL PIL PV +G+DPVHFG Sbjct: 299 QAMAAWITDSGLGPITFLLVVNILLLLAGNVMEPSSIVLILAPILFPVAMKLGIDPVHFG 358 Query: 360 MIMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISL 419 ++++VN+ +G+ PPVG L+V S I K+ I A+MP+ L + L VTY PA+SL Sbjct: 359 ILIVVNMEVGMCHPPVGLNLYVASGITKMGITELTIAVMPWLLTMLGFLALVTYWPALSL 418 Query: 420 WLPSVV 425 WLP+++ Sbjct: 419 WLPNLI 424 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: 553 Number of extensions: 35 Number of successful extensions: 4 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: 426 Length adjustment: 32 Effective length of query: 394 Effective length of database: 394 Effective search space: 155236 Effective search space used: 155236 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