Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate H281DRAFT_05541 H281DRAFT_05541 TRAP transporter, DctM subunit
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__Burk376:H281DRAFT_05541 Length = 647 Score = 253 bits (646), Expect = 1e-71 Identities = 142/423 (33%), Positives = 247/423 (58%), Gaps = 10/423 (2%) Query: 5 ILLGSFIVLILIGMPVAYALGLSALIGAWWIDIPLQAMMI---QVASGVNKFSLLAIPFF 61 +LL F+ +++G+P+A+ L LSAL+ ++I P M++ QV +G++ F LLAIPFF Sbjct: 224 MLLAGFVGGLMVGVPIAFVLALSALL--YFISDPSLPMIVYSQQVMAGMDHFVLLAIPFF 281 Query: 62 VLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSVL 121 VLAG +M GMS RL+ + G VRG ++L+ I+A+ FF +SGS +AD A+VG ++ Sbjct: 282 VLAGLVMEVNGMSSRLIELLVRIFGRVRGSMNLIAILATAFFSGVSGSKLADIAAVGGIV 341 Query: 122 IPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGLL 181 +P + R + AV + V A PP N ++ A +SI LF+AGI+P ++ Sbjct: 342 VPAVRRTKQDPNETAAVLAASGVMAETIPPCINMIIIGFVA--NISIGGLFLAGIVPAVV 399 Query: 182 LSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATES 241 ++ + L +IF KK PK R ++ G AL L+ +++I G+ SGV T+TE Sbjct: 400 MAIALATLVVIFGKKIE-PKTAFESRRPICRLLGGALVALVMVIMIGKGVTSGVATSTEV 458 Query: 242 AAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPSK 301 ++ AVV++ + F +R+ + L R + ++ +I A+S + +T++QIP+ Sbjct: 459 SSFAVVYALVIGGFTFRELTPGAIAALFVRAAAMAAGILFIIAAASSVAFALTILQIPAM 518 Query: 302 ITTAFLTLSDN-RYVILMCINFMLMLL-GTVMDMAPLILILTPILLPVITGIGVDPVHFG 359 ++ L L+ N V + ++ ++M++ G +++ AP ++I P+L+P+ +GV+P+HFG Sbjct: 519 LSAGMLALAHNYGSVAFLAVSVLIMIVFGAILEGAPALIIFGPLLVPIAVHVGVNPLHFG 578 Query: 360 MIMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISL 419 I + +G+GL +PP G L A+ IE + + + L ++L+ + +P+ISL Sbjct: 579 TIAVTAMGLGLFSPPFGLGLCATCAMTGTRIEDVSRRMFKYLALLVVMLVLLVLVPSISL 638 Query: 420 WLP 422 WLP Sbjct: 639 WLP 641 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: 792 Number of extensions: 38 Number of successful extensions: 6 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: 647 Length adjustment: 35 Effective length of query: 391 Effective length of database: 612 Effective search space: 239292 Effective search space used: 239292 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: 52 (24.6 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