Align Large component of TRAP-type D-gluconate transporter (characterized)
to candidate WP_007474714.1 CMTB2_RS05790 C4-dicarboxylate ABC transporter permease
Query= reanno::azobra:AZOBR_RS15920 (426 letters) >NCBI__GCF_000170735.1:WP_007474714.1 Length = 427 Score = 288 bits (738), Expect = 2e-82 Identities = 151/417 (36%), Positives = 253/417 (60%), Gaps = 5/417 (1%) Query: 5 VFLSSLFGL----MLLGMPIAFALMLTGVALMVHLDFFDAQL-VAQNMLSGADNYPLMAV 59 + +++LFGL +LL +P+A +L L+ + + D + ++ N+ S D Y LMA+ Sbjct: 1 MIVATLFGLFFLFLLLSVPVAVSLGLSTLITAYIFEGSDLLIDLSSNLFSQLDKYALMAI 60 Query: 60 PFFILAGELMNAGGISQRIINLAVSLVGHIRGGLGYVTIGASVMLASLSGSAIADTAALA 119 P FILAG L++ GG ++RII A + VGH+ GGL I AS++ A++SGS+ A AA+ Sbjct: 61 PMFILAGSLLSKGGSAKRIIEFAKAFVGHLPGGLPIAAIFASIIFAAVSGSSPATVAAIG 120 Query: 120 TLLIPMMRDNGYPVPRSAGLIASGGIIAPIIPPSMPFIIFGVTTNTSISGLFMAGIVPGL 179 +++ + GYP + G I + G + +IPPS+ II+GVT SI LFMAG++PG+ Sbjct: 121 SIMFGAILSAGYPKTYAIGTITTAGSLGILIPPSIVMIIYGVTAEQSIGKLFMAGVIPGI 180 Query: 180 LMGAGLVITWMFVVRGMTVKLQPKASWGERRTALVEGVWALALPVIIIGGLRGGIFTPTE 239 L+G+ L++ F + + K ASW ER E WAL VIIIGG+ GGIFTPTE Sbjct: 181 LIGSMLMLVAYFGAKRLGFKTTKPASWKERWQKFKEAFWALMTIVIIIGGIYGGIFTPTE 240 Query: 240 AAVVAAVYSLVVALFVYRQVTLKDLVPLLVQAARTTSTVMFLCAAALVSSYMVTLADLPQ 299 AA V+A+++L V+L +Y+ + +KDL + ++A+ + ++F+ A A + +Y +TL ++PQ Sbjct: 241 AAAVSAIWALFVSLVIYKDIQIKDLGNIFFESAKVSGMILFIIANASMFAYFLTLENIPQ 300 Query: 300 QMNEMLAPLLHEPKLLMVAITLLLLAVGTVMDLTPTILVLGPVLTPLAAAAGIDPTYFGV 359 + +++ + ++A+ ++LL G M+ + I+++ P+L P+A GIDP +FGV Sbjct: 301 MLTDLVVQMNLNKVTFLIAVNIILLIAGNFMEPSSIIMIMVPLLLPIAKMLGIDPIHFGV 360 Query: 360 MFVLTGTLGLIHPPVCTVLNVVCGVARISLESATRGIWPFLLTYLLLLCLLIAVPEI 416 + + LG++ PPV L V G+ S++ + + P+ + L L L+ +P+I Sbjct: 361 IITINMELGMLTPPVGLNLFVASGITGESIKEVVKSVLPWFIVMLFGLILITYIPKI 417 Lambda K H 0.328 0.142 0.420 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: 380 Number of extensions: 13 Number of successful extensions: 2 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: 427 Length adjustment: 32 Effective length of query: 394 Effective length of database: 395 Effective search space: 155630 Effective search space used: 155630 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