Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate WP_011779172.1 MVAN_RS09730 C4-dicarboxylate ABC transporter permease
Query= uniprot:E4PQE4 (729 letters) >NCBI__GCF_000015305.1:WP_011779172.1 Length = 677 Score = 263 bits (672), Expect = 2e-74 Identities = 166/535 (31%), Positives = 274/535 (51%), Gaps = 20/535 (3%) Query: 206 PVGISFAAIAGTALIMELTRRVAGMALVIIGLVFLAYVFAGPYLPG--FLGYPGLSVQRF 263 P+ ++ A+ LI+E RR G AL ++ +FLAY + G +P + + GL + Sbjct: 144 PIDVAMGALL-LVLILEACRRTTGWALPVVCAMFLAYGYYGGLMPQGWAIAHAGLDFDQI 202 Query: 264 FSQVYTD-AGILGPTTAVSSTYIILFIIFAAFLQSSKVGDYFVNFAFAAAGRSRGGPAKV 322 +Y +G G V++TYI+LF I+ A L+ S +FV+ + AA RSR + Sbjct: 203 IDALYNSGSGFFGTPLDVAATYIVLFTIYGAVLELSGGARFFVDLSVAAFRRSRSAAGRT 262 Query: 323 SIFASGLMGMINGTSAGNVVSTGSLTIPLMKKVGYSKQSAGAVEAAASTGGQIMPPIMGA 382 ++ + L+G ++G+ VS G++T P+M++ GY+ + AG V AAA G + PP +GA Sbjct: 263 TVASGFLLGTVSGSGTATAVSVGAITWPIMRRAGYTPERAGGVLAAAGVGALLSPPTLGA 322 Query: 383 GAFIMAEITGIPYTEIAIAAIIPAILYFASVYFMVDFEAAKTGMRGMREDELPKLRTMMK 442 AFI+AE + Y + A+IP +LY+ + V+ +A + GM+ + + + + Sbjct: 323 AAFIVAEYLEVSYLTVLGWAMIPTVLYYLGILLAVEIDARRFGMKPAHQQSESPWKLLAR 382 Query: 443 QCYLFVPIIILIVALFMGYSVIRAGTLATVSAAVVSWLSP-NKMGLRHILQALEIASYMA 501 Y F ++ ++V L G S RA AT A V+S+L ++ R + AL + Sbjct: 383 FGYHFSSLVAIVVLLAAGMSATRAVVYATALAFVLSFLDRWGRLTPRRLFDALSVGVRGV 442 Query: 502 IQIIVVCAAAGVIVGVISLTGVGARFSVLL---LDVAATSQLLAL----IFAMFISILLG 554 + ++ VCAAAGVI + + TG+GA+FS +L +D ++ L L +FA LLG Sbjct: 443 LPVVAVCAAAGVITAMTTKTGLGAQFSSVLVGGVDALTDNRTLMLALTAVFAAVALALLG 502 Query: 555 MGMPTTAAYAVAASVVAPGLVQLGIEPLTAHFFVFYFAVVSAITPPVALASYAAAGISGA 614 + +P TA++ + ++ P L+ L + A FVFY++V+S +TPP ALA+ A+ ++G Sbjct: 503 LAIPVTASFVIGWVIIGPALLALDVPAPAAAMFVFYYSVLSEVTPPTALAAVGASAVTGG 562 Query: 615 NAMETSVASFRIGIAAFIVPFMFFYNGA---LLMEAGWFEIARALVTATFGVYMLSGGVL 671 A+ T + R AF+VP F LL + A V A G+ LS Sbjct: 563 RAIPTMWQALRYAAPAFLVPIAFVLTAPGEYLLGRGPVLGVIWASVAACAGIVALSFAAG 622 Query: 672 GWFASISA-SWITRLLLIAAALLMIEGGLWTDLTG----IALAVLAFVIQKQRKT 721 GW + A + + R AALL++ T G + F+ K+R+T Sbjct: 623 GWVLGVGALAPVPRAFTAIAALLLLFLQPATIAAGSACLLGAVAFTFITDKRRRT 677 Lambda K H 0.327 0.139 0.410 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: 1306 Number of extensions: 72 Number of successful extensions: 5 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: 729 Length of database: 677 Length adjustment: 39 Effective length of query: 690 Effective length of database: 638 Effective search space: 440220 Effective search space used: 440220 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 (21.7 bits) S2: 54 (25.4 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