Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate GFF4127 HP15_4067 spermidine/putrescine ABC transporter ATPase subunit
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__Marino:GFF4127 Length = 362 Score = 221 bits (562), Expect = 3e-62 Identities = 137/354 (38%), Positives = 199/354 (56%), Gaps = 21/354 (5%) Query: 21 VKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKDRDIA 80 V +LD+ F +GPSGCGKTT LR++AG + +G+++I R+NDVPP R + Sbjct: 20 VDHVSLDVPAGTFFSILGPSGCGKTTLLRLLAGFDKPDQGDIHIRGERMNDVPPNRRPVN 79 Query: 81 MVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKPKALSGGQ 140 MVFQ+ AL+P MTV N+A+GLK RK+P E +R+ + + + L R P+ LSGGQ Sbjct: 80 MVFQHLALFPTMTVGDNIAYGLKRRKMPLVERRKRIARVLEQVGLPDLEHRNPQELSGGQ 139 Query: 141 RQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTEAM 200 RQRVAL R +V EP + L+DEPL LD KLR QM+ E++ L ++ TT +Y+THDQ+EAM Sbjct: 140 RQRVALARCLVLEPTLLLLDEPLGALDLKLREQMKVELKHLQKQFGTTFVYITHDQSEAM 199 Query: 201 TMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRGEIVQDGDAFYFRAP 260 M D++ VMRDG Q P+ +Y +P FVAGF+G N + GE+V D+ Sbjct: 200 VMSDQVAVMRDGRFDQVAPPEELYREPATPFVAGFVGD--NNRLSGELVSVRDSL----- 252 Query: 261 SISLRLPEG---RYGVLKASGAIGKPVVLGVRPEDL-HDEEVFMTTYPDSVLQMQVEVVE 316 LRL +G + V + G L +RPE L + + +++ + + Sbjct: 253 -AELRLDDGVLVQGRVASDNLQAGHRAELYIRPESLVLSGDALSPGFSSMQAKVRTTLFD 311 Query: 317 HMGSEVYLHTSIGPNTIVARV-----NPRHVYHVGSSVKLAIDLNKIHIFDAET 365 S V T P + AR+ PR V SS++LA + + +F AE+ Sbjct: 312 GANSRVEAETCGQP--VYARLPQDGSAPR--LSVDSSIRLAWNPSLARVFGAES 361 Lambda K H 0.321 0.138 0.395 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: 375 Number of extensions: 15 Number of successful extensions: 1 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: 384 Length of database: 362 Length adjustment: 30 Effective length of query: 354 Effective length of database: 332 Effective search space: 117528 Effective search space used: 117528 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: 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