Align C4-dicarboxylate TRAP transporter small permease protein DctQ (characterized)
to candidate WP_041097606.1 SUTH_RS05225 TRAP transporter small permease
Query= SwissProt::O07837 (227 letters) >NCBI__GCF_000828635.1:WP_041097606.1 Length = 246 Score = 204 bits (520), Expect = 9e-58 Identities = 112/221 (50%), Positives = 137/221 (61%), Gaps = 34/221 (15%) Query: 2 LRILDRAEEVLIAALIATATVLIFVSVTHRFTLGFVADFVGFFRGHGMTGAAAAAKSLYT 61 ++ LD EE LI L+ AT++IFV+V HR+ G + L Sbjct: 1 MKYLDHLEEWLITFLMGAATLIIFVAVVHRYAAGM------------------SIPGLQD 42 Query: 62 TLRGINLVWAQELCIILFVWMAKFGAAYGVRTGIHVGIDVLINRLDAPKRRFFILLGLGA 121 L +++ WAQEL II+FVWMAKFGAAYGVRTGIHVG+DVLINRLD R FI+ GL A Sbjct: 43 WLLALDMGWAQELTIIMFVWMAKFGAAYGVRTGIHVGVDVLINRLDDKVRSKFIIFGLLA 102 Query: 122 GALFTGIIATLGANFVLH--MYHA--------------SSTSPDLELPMWLVYLAIPMGS 165 GA FTGI+ TLGA FV ++A T+PDLE P W+VY AIP+G+ Sbjct: 103 GATFTGIVGTLGAFFVWDNGAHYAFLKLTGMPFGDIPEGPTTPDLEWPTWIVYSAIPLGT 162 Query: 166 SLMCFRFLQVAFGFARTGELPHHDHGHVDGVDTENEGIDAE 206 SLMCFRFLQV F RTGELPHHDHGHVDG++ +D + Sbjct: 163 SLMCFRFLQVLANFIRTGELPHHDHGHVDGLEEATPKVDID 203 Lambda K H 0.328 0.143 0.442 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: 160 Number of extensions: 6 Number of successful extensions: 3 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: 227 Length of database: 246 Length adjustment: 23 Effective length of query: 204 Effective length of database: 223 Effective search space: 45492 Effective search space used: 45492 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: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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