Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate SM_b21605 SM_b21605 sugar uptake ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF2754 (331 letters) >FitnessBrowser__Smeli:SM_b21605 Length = 362 Score = 337 bits (863), Expect = 4e-97 Identities = 182/363 (50%), Positives = 244/363 (67%), Gaps = 34/363 (9%) Query: 1 MTALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEI 60 M+ ++LT V KSFG V+V+ +++ + GEF VFVGPSGCGKSTLLR+I+GLE+ T GEI Sbjct: 1 MSGIKLTGVSKSFGAVKVIHGVDIEIGQGEFAVFVGPSGCGKSTLLRMIAGLEETTGGEI 60 Query: 61 SIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRM 120 I + VT P+KRG+AMVFQSYALYPHLSV +NMA +L R+PK EI +V A+ + Sbjct: 61 RIDAEDVTHKEPSKRGVAMVFQSYALYPHLSVFDNMAFSLSIARRPKAEIEQKVKAAAEI 120 Query: 121 LSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLH 180 L L DYLD +PS+LSGGQRQRVAIGRA+VREP++FLFDEPLSNLDA LR+ R+EIARLH Sbjct: 121 LRLSDYLDSKPSQLSGGQRQRVAIGRAIVREPRVFLFDEPLSNLDAELRVKMRMEIARLH 180 Query: 181 RQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMN 240 RQ+ A+M+YVTHDQ+EAMTLAD+IVVL+ G ++Q G P+ELY NP N FVA FIG+P MN Sbjct: 181 RQIGATMVYVTHDQVEAMTLADRIVVLKAGVVQQTGAPLELYRNPDNMFVAGFIGSPGMN 240 Query: 241 FVPAQRLGGN-----------PGQ----------------FIGIRPEYARISP-VGPLAG 272 F+ A+ + G+ PG F+G+RPE+ + G + Sbjct: 241 FLKARVVPGSGDRLTIELHDAPGVPFEIPARTGPAVGEEIFVGVRPEHITLGEREGGVGL 300 Query: 273 EVI--HVEKLGGD--TNILVDMGEDLTFTARLFGQHDTNVGETLQFDFDPANCLSFDEAG 328 +V +E+LGG + L GE++T R G+ + ++ P +F+ +G Sbjct: 301 DVTAEFIEELGGTGYLHALTVTGEEMTIECR--GEERPQPKQAVRLTLAPEEMFAFEGSG 358 Query: 329 QRI 331 +R+ Sbjct: 359 ERL 361 Lambda K H 0.320 0.137 0.391 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: 416 Number of extensions: 15 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: 331 Length of database: 362 Length adjustment: 29 Effective length of query: 302 Effective length of database: 333 Effective search space: 100566 Effective search space used: 100566 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: 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