Align Lactate utilization protein A (characterized)
to candidate WP_028314758.1 G491_RS0111850 (Fe-S)-binding protein
Query= SwissProt::O07020 (238 letters) >NCBI__GCF_000429905.1:WP_028314758.1 Length = 409 Score = 104 bits (260), Expect = 2e-27 Identities = 73/236 (30%), Positives = 107/236 (45%), Gaps = 8/236 (3%) Query: 3 VSLFVTCLVDMFQTNVGKATVELLERLGCEVDFPEGQICCGQPAYNSGYVHDAKKAMKRM 62 V+ FV C + GKA + + R G EV PEG +CCG PA G V A Sbjct: 164 VAYFVGCATNSSFVETGKALINVYTRNGIEVIVPEGLLCCGMPAIAEGDVETAYNMFMHN 223 Query: 63 IETFQDSEY--VVSPSGSCTTMFREYP-HLFQDDPKWADKAKKLADKTYELTDFIVNVLG 119 I F E VV+ +C MF+E L +K + +A K +E TD++ N LG Sbjct: 224 IRIFHKMEVDAVVTDCTTCGLMFKENGVKLAPAGTPLVEKVQGVAAKIWEATDYL-NHLG 282 Query: 120 VEDVGATLHTKATLHTSCHMTRLLGVRKEPMKLLSHVKGLQFTELPGKHNCCGFGGTFSV 179 + D A L K T H CH + P + + G + E+ CCG GGTF V Sbjct: 283 LVDQPAGLDLKFTYHEPCHRAWSPTLADAPRAVTKGIPGAELCEMAAPDACCGAGGTFFV 342 Query: 180 KMAQISEQMVDEKVECVEETGAEVLIGADCGCLMNIGGRLGRKDKNVKVMHIAEVL 235 + ++S + +K + +E+TGA+ ++ C G L + VMH ++L Sbjct: 343 QHPELSGGIRSKKTDMIEKTGADAILTQCPAC----RGYLAAGCEEKTVMHPLDLL 394 Lambda K H 0.321 0.136 0.411 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: 272 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: 238 Length of database: 409 Length adjustment: 27 Effective length of query: 211 Effective length of database: 382 Effective search space: 80602 Effective search space used: 80602 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 (21.9 bits) S2: 48 (23.1 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