Align Lactate utilization protein A (characterized)
to candidate 5210576 Shew_3004 hypothetical protein (RefSeq)
Query= SwissProt::O07020 (238 letters) >FitnessBrowser__PV4:5210576 Length = 247 Score = 164 bits (416), Expect = 1e-45 Identities = 91/249 (36%), Positives = 140/249 (56%), Gaps = 16/249 (6%) Query: 1 MKVSLFVTCLVDMFQTNVGKATVELLERLGCEVDFPEGQICCGQPAYNSGYVHDAKKAMK 60 MK++LF+ CLV+ +VG ATVELLE+LG +V P+GQ CCGQP NSG +AKK Sbjct: 1 MKIALFIPCLVNQMMPHVGIATVELLEKLGHQVILPKGQTCCGQPMTNSGCFDEAKKTTL 60 Query: 61 RMIETFQ--DSEYVVSPSGSCTTMFREYPHLFQDDPKWADKAKKLADKTYELTDFIVNVL 118 +++ F+ + + +V P+ SC +E H F D P +A+ + DK YELT+F+ +V Sbjct: 61 KLLNAFKGVECDAIVCPAASCLVAAKENFHEFDDSP----EAQAVIDKLYELTEFLHDVA 116 Query: 119 GVEDVGATLHTKATLHTSCHMTRLL---------GVRKEPMK-LLSHVKGLQFTELPGKH 168 + + K +L SCH R+L G R ++ +LS + G++ + Sbjct: 117 PIPAFNKAFNFKISLQLSCHGIRMLDLATPSEQMGPRTNKVEAVLSRIPGIEIVYPDRRD 176 Query: 169 NCCGFGGTFSVKMAQISEQMVDEKVECVEETGAEVLIGADCGCLMNIGGRLGRKDKNVKV 228 CCGFGGTF+V +S +M +K + TGA +G D CL+++ G + R+ + Sbjct: 177 ECCGFGGTFAVDEGAVSAKMGKDKAQAHAATGATYAVGFDPSCLLHLDGMIRRQLLPIAT 236 Query: 229 MHIAEVLNS 237 HIAEV+N+ Sbjct: 237 RHIAEVINA 245 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: 186 Number of extensions: 11 Number of successful extensions: 4 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: 247 Length adjustment: 23 Effective length of query: 215 Effective length of database: 224 Effective search space: 48160 Effective search space used: 48160 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: 46 (22.3 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