Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA
Query= reanno::Phaeo:GFF2754 (331 letters) >FitnessBrowser__Caulo:CCNA_03235 Length = 381 Score = 230 bits (587), Expect = 4e-65 Identities = 114/228 (50%), Positives = 156/228 (68%) Query: 8 NVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISIGGQTV 67 NV K FG + + +++LTV +GEF +GPSGCGK+TLLR+++G E T G I I GQ + Sbjct: 19 NVTKRFGKLAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPTEGRILIDGQDI 78 Query: 68 TTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRMLSLEDYL 127 + PP KR + MVFQSYA++PH++V +N+A LK + PK E ARVAEA ++ L Sbjct: 79 SNVPPNKRPVNMVFQSYAVFPHMTVADNVAYGLKVDNVPKAEREARVAEALELVQLGGLG 138 Query: 128 DRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLHRQLSASM 187 R+P +LSGGQRQRVA+ RA+V+ P++ L DEPLS LDA LR R E+ L ++ + Sbjct: 139 GRKPDQLSGGQRQRVALARALVKRPRVLLLDEPLSALDAKLREQMRTELCTLQEKVGITF 198 Query: 188 IYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIG 235 I VTHDQ EA+ LA + V+ G ++QV TP +LY P +RFVA+FIG Sbjct: 199 IMVTHDQDEALALASRCAVMSKGLLQQVATPSDLYEFPNSRFVADFIG 246 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: 326 Number of extensions: 12 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: 381 Length adjustment: 29 Effective length of query: 302 Effective length of database: 352 Effective search space: 106304 Effective search space used: 106304 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