Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate WP_090448377.1 BLS63_RS24285 L-dehydroascorbate transporter large permease subunit
Query= uniprot:Q88NP0 (426 letters) >NCBI__GCF_900100495.1:WP_090448377.1 Length = 425 Score = 282 bits (721), Expect = 2e-80 Identities = 160/429 (37%), Positives = 254/429 (59%), Gaps = 13/429 (3%) Query: 1 MEAFILLGSFIVLILIGMPVAYALGLSALIGAWWIDI-PLQAMMIQVASGVNKFSLLAIP 59 M + L S + + GMP+A+AL L+ + W+++ +Q + + +G + F LLA+P Sbjct: 1 MTVAVFLSSLLGFMAFGMPIAFALILTGAVLMWYLEFWDVQLLAQNLLAGADSFPLLAVP 60 Query: 60 FFVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGS 119 FF+LAG +M GG+S+R++A A VG RGGL V I A+ ++SGS++ADTA++ + Sbjct: 61 FFILAGELMNAGGISKRIIAMAQAYVGHKRGGLGFVAIAAAVLLASMSGSALADTAALAT 120 Query: 120 VLIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPG 179 +L+P M ++GYP S + +G + A + PPS V+Y + SI+ LFMAG++PG Sbjct: 121 LLLPMMRQRGYPLHASAGLVAAGGIIAPIIPPSMPFVIYGVVTN--TSISQLFMAGLVPG 178 Query: 180 LLLSAVMMGLCLIFAK---KRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVF 236 L++ ++ + A+ + PK R AL AL M VII+GG+ G+F Sbjct: 179 LIMGGGLIIAWSLIARGFSEPTPPKASKAERRAALVDGASAL---MLPVIIVGGLRFGIF 235 Query: 237 TATESAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLM 296 T TE+A VA V++ V+ +YR+ W L + M R RT + VM L A Y++TL Sbjct: 236 TPTEAAVVAAVYALGVSTLLYRELNWATLVEAMTRASRTTASVMFLCAAATVSAYMVTLA 295 Query: 297 QIPSKITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPV 356 Q+P +I L+++ +++ I +++ +G V+D+ P ILIL P+L P+ GVDPV Sbjct: 296 QLPDEIAAMLGPLANHPQLLVAAIMLLMIAVGMVLDLTPTILILAPVLAPIAVKAGVDPV 355 Query: 357 HFGMIMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPF---YLALFLVLMAVTY 413 +FG++ ++ IGLITPPVG VL V IG++ +E V+ +MPF YLA+ ++L+A Sbjct: 356 YFGVMFVLIGSIGLITPPVGTVLNVVGGIGRLRMEVLVRGVMPFFLVYLAIVVLLIAFPS 415 Query: 414 IPAISL-WL 421 I + L WL Sbjct: 416 IVTVPLAWL 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: 522 Number of extensions: 31 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: 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 24 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