Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate PP_1018 PP_1018 mannose/glucose ABC transporter - ATP binding subunit
Query= reanno::psRCH2:GFF857 (371 letters) >FitnessBrowser__Putida:PP_1018 Length = 384 Score = 298 bits (762), Expect = 2e-85 Identities = 174/367 (47%), Positives = 232/367 (63%), Gaps = 13/367 (3%) Query: 1 MASVTLRDICKSY-DGTPIT-RHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSG 58 MA++ LR++ K+Y G P T + I L I+DGEF++ VGPSGCGKSTL+ IAGLE IT G Sbjct: 1 MATLELRNVNKTYGSGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGG 60 Query: 59 DLLIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVA 118 +LID Q V+ + PKDR + MVFQSYALYP M+V EN+ FGLK+ + + I V VA Sbjct: 61 AILIDEQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVARVA 120 Query: 119 EILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIAR 178 ++LQ++ LL RKP LSGGQ+QRVA+GR + R PK++LFDEPLSNLDA LRV+MR E+ Sbjct: 121 KLLQIEHLLARKPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 Query: 179 LHQRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQ 238 +HQR+++T +YVTHDQ+EAMTL DK+ V+ G I Q G P +Y+ P N+FVA F+GSP Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPQQIYNDPANQFVASFIGSPP 240 Query: 239 MNFVEVRAISASPETVTIELPSGYP-LTLPVDGSA-VSPGDPLTLGIRPEHFVMPDEADF 296 MNF+ VR + + L SG LP+ +A G + LGIRPE + AD Sbjct: 241 MNFIPVRLARQDGRLLAL-LDSGQARCELPLGEAADALEGREIILGIRPEQIAL-GAADG 298 Query: 297 ----TFHGQITVAERLGQYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKADKCHL 352 ++ V E G L+++TL + + L D RV G+T + L Sbjct: 299 NGLPAIRAEVQVTEPTGPDLLVFVTLNQTKVCCRLAPDVACRV--GDTLNLQFDPARVLL 356 Query: 353 F-RENGE 358 F NGE Sbjct: 357 FDAANGE 363 Lambda K H 0.322 0.139 0.405 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: 381 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: 371 Length of database: 384 Length adjustment: 30 Effective length of query: 341 Effective length of database: 354 Effective search space: 120714 Effective search space used: 120714 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 (21.9 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