Align Lactate utilization protein A (characterized)
to candidate 7025756 Shewana3_2906 hypothetical protein (RefSeq)
Query= SwissProt::O07020 (238 letters) >FitnessBrowser__ANA3:7025756 Length = 258 Score = 155 bits (392), Expect = 7e-43 Identities = 83/249 (33%), Positives = 137/249 (55%), Gaps = 16/249 (6%) Query: 1 MKVSLFVTCLVDMFQTNVGKATVELLERLGCEVDFPEGQICCGQPAYNSGYVHDAKKAMK 60 MK++LF+ CLV+ +V AT+ELLE+LG +V P GQ CCGQP NSG A+ Sbjct: 12 MKIALFIPCLVNQMMPDVAIATLELLEKLGHQVILPAGQTCCGQPMTNSGCFDAARSTTL 71 Query: 61 RMIETFQ--DSEYVVSPSGSCTTMFREYPHLFQDDPKWADKAKKLADKTYELTDFIVNVL 118 +++ F+ + + +V P+ SC +E H F + P+ A+ + DK YELT+F+ +V Sbjct: 72 KLLNAFKGVECDAIVCPAASCLVAAKENFHEFDNSPE----AQAVIDKLYELTEFLHDVA 127 Query: 119 GVEDVGATLHTKATLHTSCHMTRLLGVRKEPMKL----------LSHVKGLQFTELPGKH 168 + K +L SCH R+L + ++ L+++ G+ + Sbjct: 128 PIPAFNKPFAHKISLQLSCHGIRMLSLATPSEQMGPRFNKVEAVLANIAGIDIVYPDRRD 187 Query: 169 NCCGFGGTFSVKMAQISEQMVDEKVECVEETGAEVLIGADCGCLMNIGGRLGRKDKNVKV 228 CCGFGGTF+V +S +M +K + TGA+ ++G D CL+++ G + R+ +++ Sbjct: 188 ECCGFGGTFAVDEGAVSAKMGKDKAQAHAATGAQYVVGFDPSCLLHLDGMIRRQQLPIEI 247 Query: 229 MHIAEVLNS 237 HIA+VLN+ Sbjct: 248 RHIAQVLNA 256 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: 177 Number of extensions: 12 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: 258 Length adjustment: 24 Effective length of query: 214 Effective length of database: 234 Effective search space: 50076 Effective search space used: 50076 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