Align Lactate utilization protein A (characterized)
to candidate WP_027456450.1 K420_RS0101260 (Fe-S)-binding protein
Query= SwissProt::Q81GA5 (239 letters) >NCBI__GCF_000519045.1:WP_027456450.1 Length = 242 Score = 224 bits (571), Expect = 1e-63 Identities = 110/237 (46%), Positives = 150/237 (63%), Gaps = 2/237 (0%) Query: 1 MKVTLFVTCLVDMFETNVGKATVEVLERLGCEIEFPEAQVCCGQPAYNSGHVEAAKEAMK 60 M+V L+VTCLVD+ +VG A + +LE GCE+ PE Q CCGQPA+++G A E K Sbjct: 1 MRVALYVTCLVDLMRPSVGFAALRLLEAAGCEVLVPEGQTCCGQPAWSAGERALAAELAK 60 Query: 61 HMIETFEDAEYIVTPSGSCATMFHE-YPHVFKDDPKWAKRAQKVADKTYEFTQFIVDVLK 119 I E + +V PSGSCA YP + DD W+ RA+ +A++ YE T F+ DVL+ Sbjct: 61 KAIGELEGYDTVVIPSGSCADQIRNIYPQLLADDAAWSARARALAERAYELTAFLADVLQ 120 Query: 120 VTDVGASLPGIATIHKSCHMTRMLGVKEAPGILLSNVKGLTVRDLPNVQNCCGFGGTFSV 179 V+ V A+ G T H SC R LG+K P LL+ V GLT++++ + CCGFGG FSV Sbjct: 121 VSAVPAAFDGSVTYHDSCKGLRSLGIKRQPRALLAKVPGLTLKEMSECEECCGFGGAFSV 180 Query: 180 KMTPISEQMVDEKVDSVMETGADYLIGADCGCLLNIGGRIERLGKE-VKVMHIAEVL 235 K +S ++VD K +S+ GAD ++G D GCL+NI GR+ R G E +V+HIAEVL Sbjct: 181 KFGDVSTKIVDRKCESIAAAGADAVVGGDLGCLMNIEGRLRRRGDETTRVLHIAEVL 237 Lambda K H 0.320 0.135 0.407 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: 163 Number of extensions: 10 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: 239 Length of database: 242 Length adjustment: 23 Effective length of query: 216 Effective length of database: 219 Effective search space: 47304 Effective search space used: 47304 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 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