Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate GFF3591 Psest_3658 spermidine/putrescine ABC transporter ATP-binding subunit
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__psRCH2:GFF3591 Length = 369 Score = 247 bits (630), Expect = 4e-70 Identities = 135/285 (47%), Positives = 182/285 (63%), Gaps = 11/285 (3%) Query: 9 IYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRR 68 I K+Y G++ V+D NLDI+ EF +GPSG GKTT+L M+AG E T G + + R Sbjct: 16 IQKSYDGESL-IVRDLNLDIRRGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEILLDGRA 74 Query: 69 VNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHL 128 +N+VPP RD+ MVFQNYAL+PHMTV +N+AF L +R + K +I RV+ A ++ + Sbjct: 75 INNVPPHKRDMGMVFQNYALFPHMTVSENLAFPLSVRGMAKPDIKERVKRALAMVQLEGF 134 Query: 129 LDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTT 188 +R P LSGGQ+QRVAL RA+V EPQ+ LMDEPL LD +LR QM+ EI+ LH+RL T Sbjct: 135 RNRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREQMQMEIKHLHERLGVT 194 Query: 189 VIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRGEI 248 V+YVTHDQ EA+TM DR+ V G IQQ + P+ +Y +P N FVA F+G N + + Sbjct: 195 VVYVTHDQGEALTMSDRVAVFHQGQIQQIEDPRTLYEKPVNTFVANFLGE--NNRLPAHL 252 Query: 249 VQDGDAFYFRAPSISLRLPEGR--YGVLKASGAIGKPVVLGVRPE 291 + R S +++L G + GA G PV L +RPE Sbjct: 253 LDR------RGDSCTVKLGRGETVEALAVNVGAAGTPVSLSIRPE 291 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: 358 Number of extensions: 13 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: 384 Length of database: 369 Length adjustment: 30 Effective length of query: 354 Effective length of database: 339 Effective search space: 120006 Effective search space used: 120006 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