Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 8500851 DvMF_1589 ABC transporter related (RefSeq)
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__Miya:8500851 Length = 354 Score = 221 bits (564), Expect = 2e-62 Identities = 136/338 (40%), Positives = 190/338 (56%), Gaps = 29/338 (8%) Query: 21 VKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVT------HVAP 74 V NLEI GE ++GPSGCGK+TTLRM+AG E++ DG I +GD+ ++ ++ P Sbjct: 19 VDSLNLEIGRGECFSMLGPSGCGKTTTLRMVAGFEDLDDGEIHVGDRLLSARRNNYYLPP 78 Query: 75 RDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPK 134 RD MVFQ +A++PH++V EN+ F L+I S EI++R EA L + ++ P Sbjct: 79 EKRDFGMVFQAFAVWPHLSVYENVAFPLRIRRLSAAEIDRRTREALHHTSLADVAQKSPD 138 Query: 135 ALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTH 194 LSGG +QRVA+ RA+ NP V L+DEPLS+LD LR + R +I LQR G + +YVTH Sbjct: 139 DLSGGGKQRVALARALAINPDVMLLDEPLSSLDPHLREEMRFEIKDLQRTFGFSILYVTH 198 Query: 195 DQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDAT 254 DQ+EA+ + DRI V+++G +QQVG P ++Y PAN FV GFIG Sbjct: 199 DQSEAMALSDRIMVMRNGVVQQVGTPLDVYTNPANSFVFGFIG----------------L 242 Query: 255 SGHARIKLSPETLAAMTPEDNGRITIGFRPEALEIIPEGESTDLSIPIKLDFVEELGSDS 314 S + L+PE L + D R+T P A ++ G + S P ++DF E G Sbjct: 243 SNFLDVNLTPEGLVRVNGGD-ARVTPATPPSA-RLVSAGRAALASRPSEIDFTAEGG--- 297 Query: 315 FLYGKLVGEGDLGSSSE-DVPESGQIVVRAAPNAAPAP 351 L G + LG + + SGQ V AP P Sbjct: 298 -LRGVVRRRAYLGEIVDYRIDVSGQEVRVQKGRRAPGP 334 Lambda K H 0.316 0.135 0.380 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: 330 Number of extensions: 14 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: 376 Length of database: 354 Length adjustment: 30 Effective length of query: 346 Effective length of database: 324 Effective search space: 112104 Effective search space used: 112104 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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