Align putative transporter, required for glycine and L-alanine utilization (characterized)
to candidate 208171 DVU2672 membrane protein, putative
Query= reanno::ANA3:7023996 (213 letters) >MicrobesOnline__882:208171 Length = 207 Score = 98.2 bits (243), Expect = 1e-25 Identities = 59/189 (31%), Positives = 89/189 (47%) Query: 12 LIGILAEAMTGALAAGRKQMDLFGVVIIGCATAIGGGTLRDMLLGNYPLIWVENVHYLLA 71 + G A A+ GAL A R ++D GV+++ T +GGG +RDM+L P N YLL Sbjct: 10 IFGTFAFAVAGALKAARHELDALGVLVLATVTGVGGGMVRDMMLAYGPPAVFHNDAYLLV 69 Query: 72 IAFASLLTVAIAPVMRYLSKLFLAIDALGLAVFSIVGAQKTLMLGFSPTIAVVMGLVTGV 131 LL A + L DA+GL VF+ +G K + G V + ++T Sbjct: 70 CLAGGLLVFFFARGVAARRNLVRYADAVGLGVFTAIGGAKAMAFGLGGLPVVFLAVLTAT 129 Query: 132 FGGVIRDILCNQVPLIFKKELYAVISLFTAGLYITLNAYQLAEWINLVVCLTLGFSLRML 191 GGVIRD+L +VP + + + YA S+ A + L A L + LR++ Sbjct: 130 GGGVIRDVLVGEVPAVLRTDFYATASILGAVALLGLAALGRPPLEQLAGSAAVTTGLRLM 189 Query: 192 ALRYHWSMP 200 A+ +P Sbjct: 190 AIWLRMRLP 198 Score = 42.0 bits (97), Expect = 8e-09 Identities = 28/92 (30%), Positives = 44/92 (47%), Gaps = 2/92 (2%) Query: 89 LSKLFLAIDALGLAVFSIVGAQKTLMLGFSPTIAVVMGLVTGVFGGVIRD-ILCNQVPLI 147 + + A+D G F++ GA K +V+ VTGV GG++RD +L P + Sbjct: 1 MQDMLYALDIFGTFAFAVAGALKAARHELDALGVLVLATVTGVGGGMVRDMMLAYGPPAV 60 Query: 148 FKKELYAVISLFTAGLYITLNAYQLAEWINLV 179 F + Y ++ L GL + A +A NLV Sbjct: 61 FHNDAYLLVCL-AGGLLVFFFARGVAARRNLV 91 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: 139 Number of extensions: 10 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: 207 Length adjustment: 21 Effective length of query: 192 Effective length of database: 186 Effective search space: 35712 Effective search space used: 35712 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