Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate 17513 b3452 glycerol-3-phosphate transporter subunit (NCBI)
Query= reanno::psRCH2:GFF850 (521 letters) >FitnessBrowser__Keio:17513 Length = 295 Score = 99.0 bits (245), Expect = 2e-25 Identities = 87/267 (32%), Positives = 132/267 (49%), Gaps = 26/267 (9%) Query: 261 PPGFTV-FTGFANFSRVLTEPSIREPFMQIFAWTFAFAGLTVVFTLAVGLVLASLLQWEL 319 P GF+ F G NF + + ++ F T F+ V L V L A+L+++ + Sbjct: 46 PFGFSSQFVGLDNFVTLFHDSY----YLDSFWTTIKFSTFVTVSGLLVSLFFAALVEY-I 100 Query: 320 VRGKAFYRLMLILPYAVPGFISILVFRGLFNQNFGEINLLLEGLFGIRPDWFSDPSLART 379 VRG FY+ +++LPYAV ++ +++ LFN G I L FG DW + + Sbjct: 101 VRGSRFYQTLMLLPYAVAPAVAAVLWIFLFNPGRGLITHFLAE-FGY--DWNHAQNSGQA 157 Query: 380 MILIV--NTWLGYPYMLLLCMGLLQAIPRDQYEASAIDGASPLDNLLRITLPQLIKPLMP 437 M L+V + W Y L LQ+IPR EA+AIDGA P+ +I LP LI P+ Sbjct: 158 MFLVVFASVWKQISYNFLFFYAALQSIPRSLIEAAAIDGAGPIRRFFKIALP-LIAPVSF 216 Query: 438 LLIA---CFAFNFNNFVLITLLTRGGPDIIGATTPAGTTDLLVSYTYRIAFQDSGQDFAL 494 L+ +AF F+ F +I T GGP + ATT L+ YR F +G D A Sbjct: 217 FLLVVNLVYAF-FDTFPVIDAATSGGP--VQATT------TLIYKIYREGF--TGLDLAS 265 Query: 495 AAAIATMIFILVGAMALLNLKLSKVKV 521 +AA + ++ LV + ++ + + KV Sbjct: 266 SAAQSVVLMFLVIVLTVVQFRYVESKV 292 Lambda K H 0.327 0.142 0.429 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: 356 Number of extensions: 11 Number of successful extensions: 2 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: 521 Length of database: 295 Length adjustment: 31 Effective length of query: 490 Effective length of database: 264 Effective search space: 129360 Effective search space used: 129360 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 (21.7 bits) S2: 50 (23.9 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