Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__Btheta:350819 Length = 463 Score = 212 bits (539), Expect = 2e-59 Identities = 122/316 (38%), Positives = 180/316 (56%), Gaps = 6/316 (1%) Query: 2 SALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDIL 61 S +E+ ++ K +G+ L + + ++ GEF+ +LG SGCGK+TLL +IAG S G+I Sbjct: 8 SIIEVSHVSKFFGDKTALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEGEIR 67 Query: 62 IGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARLL 121 I + + P R + VFQ YAL+P+L+V NI FGL++++ P+ K V+ +++ Sbjct: 68 ISGKEITQTPPHKRPVNTVFQKYALFPHLNVYDNIAFGLKLKKTPKQTIGKKVKAALKMV 127 Query: 122 QIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLHQ 181 + + R LSGGQ+QRVAI RA+V P+V L DEPL+ LD K+R +M+ ELK +H+ Sbjct: 128 GMTDYEYRDVDSLSGGQQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKDMQMELKEMHK 187 Query: 182 MLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMNI 241 L T VYVTHDQ EA+TL+ I VM +G+I+Q+ P ++Y+ P +VA F+G NI Sbjct: 188 SLGITFVYVTHDQEEALTLSDTIVVMSEGKIQQIGTPIDIYNEPINSFVADFIGE--SNI 245 Query: 242 LDAEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRLTASVE 301 L+ M + L E + F V V IRPE L + SE +LT V+ Sbjct: 246 LNGTMIHDKLVRFCGTEFECVDEGFG----ENTPVDVVIRPEDLYIFPVSEMAQLTGVVQ 301 Query: 302 VVELTGPELVTTATVG 317 G T G Sbjct: 302 TSIFKGVHYEMTVLCG 317 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: 353 Number of extensions: 10 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: 360 Length of database: 463 Length adjustment: 31 Effective length of query: 329 Effective length of database: 432 Effective search space: 142128 Effective search space used: 142128 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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