Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate GFF4209 Psest_4282 spermidine/putrescine ABC transporter ATP-binding subunit
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__psRCH2:GFF4209 Length = 383 Score = 221 bits (563), Expect = 3e-62 Identities = 119/274 (43%), Positives = 173/274 (63%), Gaps = 6/274 (2%) Query: 21 VKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKDRDIA 80 V D +L I E +G SG GK+T LRM+AG E TEG +++ + + D+PP +R I Sbjct: 38 VDDVSLSIHQGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIFLDGQDITDMPPYERPIN 97 Query: 81 MVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKPKALSGGQ 140 M+FQ+YAL+PHMTV QN+AFGLK +PKAEI+ RV+E ++ + RKP LSGGQ Sbjct: 98 MMFQSYALFPHMTVEQNIAFGLKQDGLPKAEIEERVKEMLGLVQMTQYAKRKPHQLSGGQ 157 Query: 141 RQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTEAM 200 RQRVAL R++ + P++ L+DEP+ LD KLR QM+ E+ ++ +R+ T + VTHDQ EAM Sbjct: 158 RQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELVQIIERVGVTCVMVTHDQEEAM 217 Query: 201 TMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRGEIVQD-GDAFYFRA 259 TM +RI +M G I Q +P +Y P + V FIG+ +N GE+++D GD + Sbjct: 218 TMAERIAIMHLGWIAQVGSPMDIYETPASRLVCEFIGN--VNLFDGELIEDMGDHAVIAS 275 Query: 260 PSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDL 293 P + + G +G+ ++ A K + +RPE L Sbjct: 276 PGLENPIYVG-HGI--STRAEDKQITYAIRPEKL 306 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: 345 Number of extensions: 10 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: 383 Length adjustment: 30 Effective length of query: 354 Effective length of database: 353 Effective search space: 124962 Effective search space used: 124962 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