Align putative transporter, required for glycine and L-alanine utilization (characterized)
to candidate 5208645 Shew_1154 hypothetical protein (RefSeq)
Query= reanno::ANA3:7023996 (213 letters) >FitnessBrowser__PV4:5208645 Length = 217 Score = 355 bits (911), Expect = e-103 Identities = 176/217 (81%), Positives = 195/217 (89%), Gaps = 4/217 (1%) Query: 1 MQEAQFIGLLWLIGILAEAMTGALAAGRKQMDLFGVVIIGCATAIGGGTLRDMLLGNYPL 60 MQEA+FI LLWLIGILAEAMTGAL AGRKQMDLFGVVIIGCATAIGGGTLRD+LLGNYPL Sbjct: 1 MQEAEFITLLWLIGILAEAMTGALCAGRKQMDLFGVVIIGCATAIGGGTLRDILLGNYPL 60 Query: 61 IWVENVHYLLAIAFASLLTVAIAPVMRYLSKLFLAIDALGLAVFSIVGAQKTLMLGFSPT 120 IWVEN+HYLLAIAFASLLTV I+PVMRYLSKLFLAIDALGLAVFSIVGAQKTL+LGFSPT Sbjct: 61 IWVENIHYLLAIAFASLLTVIISPVMRYLSKLFLAIDALGLAVFSIVGAQKTLLLGFSPT 120 Query: 121 IAVVMGLVTGVFGGVIRDILCNQVPLIFKKELYAVISLFTAGLYITLNAYQLAEWINLVV 180 +A+VMG+VTGVFGGVIRDILCNQVPLIFKKELYA++SL TA LY+ L ++++ EWINL + Sbjct: 121 LAIVMGVVTGVFGGVIRDILCNQVPLIFKKELYALVSLTTASLYMLLRSFEVTEWINLAI 180 Query: 181 CLTLGFSLRMLALRYHWSMPTFDYQ----ANGDQHTH 213 L++GFS RMLA+RYHW MP FDYQ N D H Sbjct: 181 SLSVGFSFRMLAIRYHWGMPKFDYQHGDHGNQDSQAH 217 Lambda K H 0.330 0.143 0.438 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: 239 Number of extensions: 4 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: 213 Length of database: 217 Length adjustment: 22 Effective length of query: 191 Effective length of database: 195 Effective search space: 37245 Effective search space used: 37245 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 (21.8 bits) S2: 45 (21.9 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