Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate SM_b21351 SM_b21351 C4-dicarboxylate large membrane transport protein
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__Smeli:SM_b21351 Length = 427 Score = 406 bits (1043), Expect = e-118 Identities = 200/428 (46%), Positives = 299/428 (69%), Gaps = 8/428 (1%) Query: 1 MEAFILLGSFIVLILIGMPVAYALGLSALIGAWWIDIPLQAMMIQVASGVNKFSLLAIPF 60 M+ IL G F +L+LIG P+A+ LG+++ ++ +P + ++ SG++ FSLLAIPF Sbjct: 1 MDMMILFGVFTLLMLIGTPIAFCLGVASFATVLYLGLPPLVIFQRLNSGMSVFSLLAIPF 60 Query: 61 FVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSV 120 F+ AG +M GG+++++VAFA LVG +RGGL VNI+ +T FG ISGS+VA+ A+VG + Sbjct: 61 FIYAGDLMVRGGIAQKIVAFAASLVGHIRGGLGQVNIVTATLFGGISGSAVAEAAAVGGL 120 Query: 121 LIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGL 180 +IP+M+++GY +++ VT ++ AL+ PPSHN ++YS++AGG +SIA LF AGI+PGL Sbjct: 121 MIPQMKQRGYGADYAVNVTSMAALIALMLPPSHNMIIYSISAGGKISIADLFTAGILPGL 180 Query: 181 LLSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALW----GLMAMVIILGGILSGVF 236 L +A +M A++R YP EV P G L GL+ + II GG+ SGVF Sbjct: 181 LYAAALMATAYFVARRRGYPT-EVFP---GFARVGRYLLISTPGLLLIGIIFGGVRSGVF 236 Query: 237 TATESAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLM 296 TATES+ +AV+++ VT+F+YR W+D + VRT ++V+++IG AA+F ++M + Sbjct: 237 TATESSCIAVLYALAVTVFVYRQMTWQDFVQATFAAVRTTAMVLLIIGMAAAFSWLMAFL 296 Query: 297 QIPSKITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPV 356 ++P+ + T+S+N +IL+ +N +++ LGT MDM P I+I TPI LPV GVDPV Sbjct: 297 RVPAALIDWMNTISENPIIILLLLNVLMLFLGTFMDMGPTIIICTPIFLPVAMAYGVDPV 356 Query: 357 HFGMIMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPA 416 HFG+IM++N GIGL TPPVGAV FV A+GK+S+ ++++ PFYLA +VL VTY+PA Sbjct: 357 HFGVIMILNFGIGLNTPPVGAVQFVACAVGKISVWEAMRSIWPFYLAGLIVLGLVTYVPA 416 Query: 417 ISLWLPSV 424 +SLWLP+V Sbjct: 417 LSLWLPAV 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: 571 Number of extensions: 30 Number of successful extensions: 3 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: 427 Length adjustment: 32 Effective length of query: 394 Effective length of database: 395 Effective search space: 155630 Effective search space used: 155630 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