Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate WP_047006259.1 AAW01_RS05635 ABC transporter ATP-binding protein
Query= reanno::BFirm:BPHYT_RS16095 (369 letters) >NCBI__GCF_001010925.1:WP_047006259.1 Length = 233 Score = 124 bits (310), Expect = 3e-33 Identities = 79/205 (38%), Positives = 115/205 (56%), Gaps = 15/205 (7%) Query: 17 EVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDLTIDG-----MRVNDVA 71 E++R I+L + GE + +GPSG GKS+LM ++ GLE SGG L + G + + +A Sbjct: 28 EILRGIDLSVQQGETLALLGPSGSGKSSLMSVLTGLERASGGSLLVAGEDFTALDEDALA 87 Query: 72 PAKRG-IAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAKILH---IDHLL 127 A+RG I +V Q++ L P M+ +N+A ++LAG DAA AA L + H L Sbjct: 88 MARRGRIGIVLQAFHLLPTMSAVENVATPMELAGD-----DAAWEKAAAELESVGLGHRL 142 Query: 128 DRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARLHDELKTTM 187 P QLSGG++QRVAI RAI +P + DEP NLD A + R DE T+ Sbjct: 143 THYPTQLSGGEQQRVAIARAIAPRPPLIFADEPTGNLDTATGTDVENVLFRRRDETGATL 202 Query: 188 IYVTHDQVEAMTLADKIVVLSAGNL 212 I +THD+ + ++V L+ G + Sbjct: 203 IIITHDR-KLAERCGRVVTLADGKI 226 Lambda K H 0.320 0.135 0.384 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: 197 Number of extensions: 9 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: 369 Length of database: 233 Length adjustment: 26 Effective length of query: 343 Effective length of database: 207 Effective search space: 71001 Effective search space used: 71001 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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