Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate GFF2081 Psest_2124 TRAP transporter, DctM subunit
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__psRCH2:GFF2081 Length = 425 Score = 294 bits (752), Expect = 4e-84 Identities = 152/418 (36%), Positives = 255/418 (61%), Gaps = 3/418 (0%) Query: 1 MEAFILLGSFIVLILIGMPVAYALGLSALIGAWWIDI-PLQAMMIQVASGVNKFSLLAIP 59 M + L S + + +GMP+A+AL L+ + W++D +Q + + +G + F LLA+P Sbjct: 1 MTVVVFLSSLLGFMTLGMPIAFALLLTGSVLMWYLDFWDVQLLAQNLQAGADSFPLLAVP 60 Query: 60 FFVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGS 119 FF+LAG +M GG+SRR++A A G RGGL V I AS ++SGS++ADTA++ + Sbjct: 61 FFILAGELMNAGGISRRIIAMAQAYFGHKRGGLGYVAIAASVLLASMSGSALADTAALAT 120 Query: 120 VLIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPG 179 +L+P M +GYP S+ + +G + A + PPS V+Y + G SI+ LF+AG++PG Sbjct: 121 LLLPMMRERGYPLSSSSGLVAAGGIIAPIIPPSMPFVIYGVVTG--TSISQLFLAGMVPG 178 Query: 180 LLLSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTAT 239 L++ ++ + A++ + PK E E ++ + LM VII+GG+ G+FT T Sbjct: 179 LIMGMGLIVAWTLIARRIDEPKQEKASAAERRRVLVDGAAALMLPVIIVGGLRGGLFTPT 238 Query: 240 ESAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIP 299 E+A VA V++ V+ +YR+ W L +++ R RT + VM L A Y++TL Q+P Sbjct: 239 EAAVVAAVYALAVSTLLYRELNWAGLVEVLTRASRTTASVMFLCAAATVSAYMITLAQLP 298 Query: 300 SKITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFG 359 +I L+ + ++++ I +++ +G V+D+ P ILIL P+L P+ G+DPV+FG Sbjct: 299 DEIAAMLGPLAQDPKLLMVAIMLLMIAVGMVLDLTPTILILGPVLAPIAIKAGIDPVYFG 358 Query: 360 MIMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAI 417 ++ ++ IGLITPPVG VL V IG++ +E+ V+ +MPF+L +++ + +P+I Sbjct: 359 VMFVLIGSIGLITPPVGTVLNVVGGIGRLRMETLVRGVMPFFLIYLVIVGLLIAVPSI 416 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: 537 Number of extensions: 27 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: 425 Length adjustment: 32 Effective length of query: 394 Effective length of database: 393 Effective search space: 154842 Effective search space used: 154842 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