Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate SMc01626 SMc01626 ABC transporter permease
Query= reanno::psRCH2:GFF851 (296 letters) >FitnessBrowser__Smeli:SMc01626 Length = 285 Score = 128 bits (321), Expect = 2e-34 Identities = 93/284 (32%), Positives = 147/284 (51%), Gaps = 19/284 (6%) Query: 19 ALLAFVAAILFPLLMVISISFREGNFATGSLFPEN----PTLEHWSLALGIPYTHADGSV 74 AL V +FP++ + +SF+ T P + PTLE+++ + A G++ Sbjct: 15 ALTLVVVFFMFPIVWIFLMSFQTNE--TILRIPPSVVFTPTLENYAALITGKLQTASGTL 72 Query: 75 TQPPFPVLLWLWNSVKIAFVSSILILLLSTTSAYAFARMRFGGKAPILKSMLIFQMFPPV 134 + L NSV ++ S L L+L +AYAFAR +F G I ++L F+ PP+ Sbjct: 73 D---IAFMRNLGNSVLLSVASVALALVLGVPAAYAFARHKFRGSEDIAFTLLSFRFAPPL 129 Query: 135 LSLVAIYALFDQLGQHVSWLGVNS--HGAVIVASLGGMALHIWTIKGYFESIDASLEEAA 192 L L+ L Q+ WLG+++ G + + L + L +W ++GYFE I A +E A Sbjct: 130 LVLLP-------LTQYFQWLGLSNTYFGLIWIYQLICLPLILWIVRGYFEDISADVEYAY 182 Query: 193 IVDGATTWQAFFHILLPMSVPILAVVFILAFITSVTEYPIASVLLMDVDKLTLSVGAQQY 252 + G + + F I LP++ P +A +LAFI + + A VL DK ++VGA + Sbjct: 183 RIAGHSWFSTFRKIALPLAGPGIAAAGLLAFIFAWNNFVFALVLA-SADKQPVTVGALAF 241 Query: 253 LYPQNYLWGDFAAAAVLSGLPITAVFLYCQKWIVGGLTAGGVKG 296 + +G AAA VLS P A+ LY Q+++V GL+ G VKG Sbjct: 242 VTASGIQYGQIAAAIVLSITPTLALALYAQRYLVEGLSLGAVKG 285 Lambda K H 0.327 0.139 0.433 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: 276 Number of extensions: 15 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: 296 Length of database: 285 Length adjustment: 26 Effective length of query: 270 Effective length of database: 259 Effective search space: 69930 Effective search space used: 69930 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: 48 (23.1 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