Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate WP_049989147.1 LT39_RS03805 TRAP transporter large permease
Query= uniprot:Q88NP0 (426 letters) >NCBI__GCF_000784335.1:WP_049989147.1 Length = 431 Score = 276 bits (705), Expect = 1e-78 Identities = 149/424 (35%), Positives = 253/424 (59%), Gaps = 6/424 (1%) Query: 4 FILLGSFIVLILIGMPVAYALGLSALIGAWWIDIPLQAMMIQ--VASGVNKFSLLAIPFF 61 FIL+ + L LIG+PVA+ALGL++LI + ++ + SG + F LLAIP F Sbjct: 9 FILV--LLALYLIGVPVAFALGLTSLILMLTPMVSYSPELVAQTLVSGADSFVLLAIPLF 66 Query: 62 VLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSVL 121 +L G M G++ + FA ++G +RGG++ VNI+AS F ++G++ AD A +G++ Sbjct: 67 LLTGLYMNSFGLTSIIFDFAEEMIGPIRGGIAHVNILASILFSGMTGTAAADAAGLGAIE 126 Query: 122 IPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGLL 181 M+ GY + +S AVT S ++ + PPS ++Y + A VSI LF+AGI+PGL+ Sbjct: 127 YEAMQDAGYEKGYSAAVTGSSAIIGPIIPPSVPLIMYGILA--QVSIGVLFIAGIVPGLI 184 Query: 182 LSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATES 241 + A ++ LC +A Y +G L + + A L V+I+GG+L G FTATE+ Sbjct: 185 MGATLLMLCTYYAHSHGYERGTWWSLPDIWESFKTAAPALGTPVLIIGGLLGGFFTATEA 244 Query: 242 AAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPSK 301 AVA+ ++ FV Y + D + + V T + + ++ A +G+++ Q+P Sbjct: 245 GAVALFYTLFVGYVFYGGVENGDFVETTYEGVVTTAALTFIVASATLYGFLVRRAQLPDA 304 Query: 302 ITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFGMI 361 + A + ++ + ++L+ I +L+++G +M+ I ILTP+ LPVI G+DP+HFG++ Sbjct: 305 LAEAVIGVTGDPTLLLLMIVGVLLIVGLMMETIAAITILTPVFLPVIDVAGIDPIHFGIV 364 Query: 362 MLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISLWL 421 M++ L IGL+TPP G +LF+ + V +E +++++PFY+ L ++L+ V +P ++LWL Sbjct: 365 MILTLMIGLLTPPFGIILFILEKVTDVGLERIMRSMVPFYIPLLIILLLVVVLPGLTLWL 424 Query: 422 PSVV 425 P V Sbjct: 425 PKFV 428 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: 607 Number of extensions: 30 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: 431 Length adjustment: 32 Effective length of query: 394 Effective length of database: 399 Effective search space: 157206 Effective search space used: 157206 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