Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_008509836.1 BIBO1_RS16200 ABC transporter ATP-binding protein
Query= reanno::psRCH2:GFF857 (371 letters) >NCBI__GCF_000182725.1:WP_008509836.1 Length = 333 Score = 329 bits (843), Expect = 8e-95 Identities = 185/361 (51%), Positives = 231/361 (63%), Gaps = 31/361 (8%) Query: 1 MASVTLRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDL 60 MA + LRD+ KS+ + + +D+DI GEF+VFVGPSGCGKSTLLRLIAGLE+ITSG L Sbjct: 1 MAELQLRDVRKSFGSFEVIKGVDMDIRPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTL 60 Query: 61 LIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEI 120 I+ VN+ P R + MVFQSYALYPHMTV ENMAFG++LAS ++E K R+ A AE+ Sbjct: 61 SINGAVVNNFNPSRRGIAMVFQSYALYPHMTVYENMAFGMQLASKSRQECKARIHAAAEM 120 Query: 121 LQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLH 180 LQL LER P+ LSGGQRQRVAIGR +VR+PKVFLFDEPLSNLDA LRV R+EIARLH Sbjct: 121 LQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIARLH 180 Query: 181 QRIR-STMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQM 239 Q + +TMIYVTHDQVEAMTLAD+I VL G + Q+G PL LY P + FVAGF+GSP+M Sbjct: 181 QSMEDTTMIYVTHDQVEAMTLADRICVLRDGRVEQIGTPLELYEKPNSLFVAGFIGSPKM 240 Query: 240 NFVEVRAISASPETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRPEHF-VMPDEADFTF 298 NF + G P T+G+R EH ++P+ ++ Sbjct: 241 NF--------------------------LTGPHAEPFGAHTVGLRSEHLAIVPERGHWS- 273 Query: 299 HGQITVAERLGQYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKADKCHLFRENGE 358 GQ+ E LG +Y+ L L++ + + G GE + D H F E G Sbjct: 274 -GQVVHTEILGSDTYVYIDL-GLEEPLVVRESGVSARKPGEALSISPTGDHVHRFDEKGR 331 Query: 359 A 359 A Sbjct: 332 A 332 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: 337 Number of extensions: 20 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: 371 Length of database: 333 Length adjustment: 29 Effective length of query: 342 Effective length of database: 304 Effective search space: 103968 Effective search space used: 103968 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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