Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate Ac3H11_3036 Fructose ABC transporter, permease component FrcC
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3036 Length = 319 Score = 198 bits (503), Expect = 2e-55 Identities = 116/305 (38%), Positives = 177/305 (58%), Gaps = 5/305 (1%) Query: 40 FASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTF 99 F +L+L FF+ S F+ N ILQ V V+AI T VI+T+GIDLS G +M Sbjct: 17 FIALILACAFFATQSERFLSAQNFALILQQVMVVAVIAIGQTLVILTAGIDLSCGMVMAL 76 Query: 100 CAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLKGLS 159 ++ + ++G+ P+ IA + L G I+G+++ K+K+PPFI TLG + + + Sbjct: 77 GGIVMTKMAADYGLSAPVAIACGMAVTMLFGLINGLLVTKIKLPPFIVTLGTLNIAFAAT 136 Query: 160 LVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASIILNKTVFGR 219 + SG + I + G +A+ +G + + AVL+L L + L +T GR Sbjct: 137 QLYSGAQTIT-DIPAGMTALGNTFQLGQ---TAIVWGAVLMLALYLV-TWFALRETAPGR 191 Query: 220 YTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELDA 279 + +A+G++ EA RL+G+ D + VY +G GIA L+ +R + P GQ LDA Sbjct: 192 HVYAVGNSPEATRLTGIATDKVLLGVYVLAGLFYGIASLLSVARTGAGDPNAGQTENLDA 251 Query: 280 IAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIIILAVYLD 339 I+AVV+GGTSL GG G ILGT++GA I+ V NGL +M V+ +Q +VTG+++ILAV D Sbjct: 252 ISAVVLGGTSLFGGRGVILGTLVGALIVGVFRNGLTLMGVSSVYQILVTGILVILAVATD 311 Query: 340 ILRRR 344 L R+ Sbjct: 312 QLSRK 316 Lambda K H 0.326 0.139 0.398 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: 225 Number of extensions: 11 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: 347 Length of database: 319 Length adjustment: 28 Effective length of query: 319 Effective length of database: 291 Effective search space: 92829 Effective search space used: 92829 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: 49 (23.5 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