Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate GFF4127 HP15_4067 spermidine/putrescine ABC transporter ATPase subunit
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__Marino:GFF4127 Length = 362 Score = 216 bits (551), Expect = 6e-61 Identities = 134/360 (37%), Positives = 195/360 (54%), Gaps = 13/360 (3%) Query: 2 SALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDIL 61 S L + +R+G + + + + +G F +LG SGCGK+TLL ++AG +P GDI Sbjct: 3 SDLFCEGLVRRFGSNAAVDHVSLDVPAGTFFSILGPSGCGKTTLLRLLAGFDKPDQGDIH 62 Query: 62 IGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARLL 121 I + V P R + MVFQ AL+P ++V NI +GL+ R++P E K + + Sbjct: 63 IRGERMNDVPPNRRPVNMVFQHLALFPTMTVGDNIAYGLKRRKMPLVERRKRIARVLEQV 122 Query: 122 QIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLHQ 181 + +L R P +LSGGQRQRVA+ R LV P + L DEPL LD KLR +M+ ELK L + Sbjct: 123 GLPDLEHRNPQELSGGQRQRVALARCLVLEPTLLLLDEPLGALDLKLREQMKVELKHLQK 182 Query: 182 MLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMNI 241 TT VY+THDQ EAM ++ ++AVMRDGR +Q+A P+E+Y PAT +VAGFVG N Sbjct: 183 QFGTTFVYITHDQSEAMVMSDQVAVMRDGRFDQVAPPEELYREPATPFVAGFVGD--NNR 240 Query: 242 LDAEMTA---NGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEA---QR 295 L E+ + + ++ + VL + AG R ++ IRPE+L L+ + + Sbjct: 241 LSGELVSVRDSLAELRLDDGVLVQGRVASDNLQAGHRAELYIRPESLVLSGDALSPGFSS 300 Query: 296 LTASVEVVELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHLFDPESGR 355 + A V G A Q + A LP GSA + D + ++P R Sbjct: 301 MQAKVRTTLFDGANSRVEAETCGQPVYARLPQD-----GSAPRLSVDSSIRLAWNPSLAR 355 Lambda K H 0.320 0.136 0.385 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: 328 Number of extensions: 15 Number of successful extensions: 3 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: 360 Length of database: 362 Length adjustment: 29 Effective length of query: 331 Effective length of database: 333 Effective search space: 110223 Effective search space used: 110223 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