Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate GFF3591 Psest_3658 spermidine/putrescine ABC transporter ATP-binding subunit
Query= reanno::Smeli:SMc02869 (352 letters) >FitnessBrowser__psRCH2:GFF3591 Length = 369 Score = 224 bits (571), Expect = 3e-63 Identities = 125/317 (39%), Positives = 190/317 (59%), Gaps = 32/317 (10%) Query: 20 LQLKTIRKAF-GSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSVQI 78 + + I+K++ G +++ ++LD++ GEF+ +GPSG GK+T L +AG E T+G + + Sbjct: 11 VSFRGIQKSYDGESLIVRDLNLDIRRGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEILL 70 Query: 79 DGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGMLS 138 DG + +V P KR + MVFQ+YAL+PH+TV +N+ L G+ K +I+E+V +A M+ Sbjct: 71 DGRAINNVPPHKRDMGMVFQNYALFPHMTVSENLAFPLSVRGMAKPDIKERVKRALAMVQ 130 Query: 139 LEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLHRS 198 LE + R PA+LSGGQ+QRVA+ RA+V EP+L L DEPL LD LR ++EI LH Sbjct: 131 LEGFRNRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREQMQMEIKHLHER 190 Query: 199 LKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQMNFI 258 L T++YVTHDQ EA+T++D++ V + G+I+Q+ P LY +P N FVA F+G + N + Sbjct: 191 LGVTVVYVTHDQGEALTMSDRVAVFHQGQIQQIEDPRTLYEKPVNTFVANFLG--ENNRL 248 Query: 259 EA-----------AKLGDGEA--------------KTIGIRPEHIGLSRESGD----WKG 289 A KLG GE ++ IRPE + L+ S + + G Sbjct: 249 PAHLLDRRGDSCTVKLGRGETVEALAVNVGAAGTPVSLSIRPERVLLNGASANCPNRFTG 308 Query: 290 KVIHVEHLGADTIIYIE 306 +V +LG I +E Sbjct: 309 RVAEFIYLGDHIRIRLE 325 Lambda K H 0.320 0.137 0.393 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: 317 Number of extensions: 13 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: 352 Length of database: 369 Length adjustment: 29 Effective length of query: 323 Effective length of database: 340 Effective search space: 109820 Effective search space used: 109820 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