Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate GFF3591 Psest_3658 spermidine/putrescine ABC transporter ATP-binding subunit
Query= SwissProt::Q9YGA6 (372 letters) >FitnessBrowser__psRCH2:GFF3591 Length = 369 Score = 241 bits (614), Expect = 3e-68 Identities = 120/239 (50%), Positives = 169/239 (70%), Gaps = 9/239 (3%) Query: 14 GEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIGDKLVADPEKG 73 GE VR+++L+++ GEF+ LLGPSG GKTT+L M+AG E P+ G+I + + + + Sbjct: 22 GESLIVRDLNLDIRRGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEILLDGRAINN---- 77 Query: 74 IFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVREVAELLGLTELL 133 VPP RD+ MVFQ+YAL+PHMTV +N+AFPL +R + + +I +RV+ ++ L Sbjct: 78 --VPPHKRDMGMVFQNYALFPHMTVSENLAFPLSVRGMAKPDIKERVKRALAMVQLEGFR 135 Query: 134 NRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKKLQRQLGVTT 193 NR P +LSGGQ+QRVAL RA+V +PQ+ LMDEPL LD +LR +M+ E+K L +LGVT Sbjct: 136 NRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREQMQMEIKHLHERLGVTV 195 Query: 194 IYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIGSP---PMNFLD 249 +YVTHDQ EA+TM DR+AV ++G +QQ+ P +Y+KP NTFVA F+G P + LD Sbjct: 196 VYVTHDQGEALTMSDRVAVFHQGQIQQIEDPRTLYEKPVNTFVANFLGENNRLPAHLLD 254 Lambda K H 0.323 0.142 0.406 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: 367 Number of extensions: 15 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: 372 Length of database: 369 Length adjustment: 30 Effective length of query: 342 Effective length of database: 339 Effective search space: 115938 Effective search space used: 115938 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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