Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate Ac3H11_2555 Glutamine ABC transporter, periplasmic glutamine-binding protein (TC 3.A.1.3.2)
Query= uniprot:A0A1N7UK26 (258 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2555 Length = 249 Score = 102 bits (253), Expect = 1e-26 Identities = 78/251 (31%), Positives = 122/251 (48%), Gaps = 16/251 (6%) Query: 4 LRSLFAALLLPLCATAHAQEWKEIRFGVFPEYPPFESVAADGSLQGFDIELGNAICAKLE 63 L SL AA C T + +R G +PP E V +G GFDIEL AI + Sbjct: 9 LASLAAAAF---CTTGAQAQDNVLRVGTDATFPPMEFVE-NGKRTGFDIELVEAIAKTMG 64 Query: 64 VKCTWVHNEFDGMIPALRARKFDAIMSSMAVTPAREKIIDFSDRLFLSPTSVITRKSADF 123 + WV +F G+IP L +++FD +S++ +T R+K++DF+D + V+ + Sbjct: 65 KQVEWVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYAGGLVVMVKADNKA 124 Query: 124 GDTPESLMGKQVGVLQGSLQEAYARAHLAKLGAQIKAYQSQDQ-NYADLQNGRLDATLTD 182 + L GK+V V G+ +Y K+ +++ ++Q+ N D+ GR DA +T Sbjct: 125 INKLADLDGKKVSVQVGTKSVSYLTEKFPKV-QRVEVEKNQEMFNLVDI--GRADAAVTG 181 Query: 183 KLEAQLNFLSKPEGSDFKTGPAFKDPTLPL-DIAMGLRKNDQALRALINKGIAAVQADGT 241 K A ++P G D L + M LRK+ L +N I ++ADGT Sbjct: 182 KPAAFQYVRTRP-------GLRVLDEQLTTEEYGMALRKDTPELTKAVNGAITKLKADGT 234 Query: 242 YAQIQKKYFGD 252 YA I KK+F + Sbjct: 235 YAAIVKKWFSN 245 Lambda K H 0.319 0.135 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: 147 Number of extensions: 5 Number of successful extensions: 2 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: 258 Length of database: 249 Length adjustment: 24 Effective length of query: 234 Effective length of database: 225 Effective search space: 52650 Effective search space used: 52650 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: 47 (22.7 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