Align putative transporter, required for glycine and L-alanine utilization (characterized)
to candidate BPHYT_RS08720 BPHYT_RS08720 membrane protein
Query= reanno::ANA3:7023996 (213 letters) >FitnessBrowser__BFirm:BPHYT_RS08720 Length = 208 Score = 117 bits (293), Expect = 2e-31 Identities = 67/190 (35%), Positives = 104/190 (54%), Gaps = 1/190 (0%) Query: 12 LIGILAEAMTGALAAGRKQMDLFGVVIIGCATAIGGGTLRDMLLGNYPLIWVENVHYLLA 71 L G + A+ GAL+A +DL GV++I A+GGG +RD+L+G+ P + + Y Sbjct: 14 LAGTVVFALEGALSAIHGGLDLLGVMVIAFVAALGGGVIRDLLIGDSPPNAIRDWRYPAL 73 Query: 72 IAFASLLTVAI-APVMRYLSKLFLAIDALGLAVFSIVGAQKTLMLGFSPTIAVVMGLVTG 130 LLT + ++ L +DA GLA+F++ G +K L+ G P IA++MG VTG Sbjct: 74 TFITGLLTFIFHSTAQQFPVALVTVLDAAGLALFAVAGVEKALLFGIRPFIAMLMGTVTG 133 Query: 131 VFGGVIRDILCNQVPLIFKKELYAVISLFTAGLYITLNAYQLAEWINLVVCLTLGFSLRM 190 V GGVIRD+L +VPL+ ++YA + A + + L + + F LR+ Sbjct: 134 VGGGVIRDVLLARVPLVLHADIYATAAFAGAFIVVVARRAGLPPGAAALAGGSACFVLRV 193 Query: 191 LALRYHWSMP 200 LA+ Y W +P Sbjct: 194 LAVTYGWHLP 203 Score = 35.8 bits (81), Expect = 6e-07 Identities = 20/54 (37%), Positives = 27/54 (50%) Query: 92 LFLAIDALGLAVFSIVGAQKTLMLGFSPTIAVVMGLVTGVFGGVIRDILCNQVP 145 L LA D G VF++ GA + G +V+ V + GGVIRD+L P Sbjct: 8 LVLAADLAGTVVFALEGALSAIHGGLDLLGVMVIAFVAALGGGVIRDLLIGDSP 61 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: 116 Number of extensions: 8 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 213 Length of database: 208 Length adjustment: 21 Effective length of query: 192 Effective length of database: 187 Effective search space: 35904 Effective search space used: 35904 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