Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate GFF3832 PGA1_262p02360 putative histidine-binding periplasmic protein
Query= uniprot:A0A1N7UK26 (258 letters) >FitnessBrowser__Phaeo:GFF3832 Length = 259 Score = 170 bits (431), Expect = 2e-47 Identities = 101/255 (39%), Positives = 149/255 (58%), Gaps = 10/255 (3%) Query: 7 LFAALLLPLCATAHAQEWKEIRFGVFPE-YPPFESVAADGSLQGFDIELGNAICAKLEVK 65 L AA + CA A A+ ++ GV E YPPF S+ + G G++I++ NA+CA E+ Sbjct: 12 LAAATVAATCAVAQAEP---VKIGVAAEPYPPFASLDSSGQWVGWEIDVINAVCAAAELD 68 Query: 66 CTWVHNEFDGMIPALRARKFDAIMSSMAVTPAREKIIDFSDRLFLSPTSVITRKSADFGD 125 C +DG+IP+L ++ DAIM+SM++T R K IDFSD + +P ++ KS D Sbjct: 69 CVITPVAWDGIIPSLTGQQVDAIMASMSITEERLKTIDFSDPYYNTPAVIVADKSMDIEA 128 Query: 126 TPESLMGKQVGVLQGSLQEAYARAHLAKLGAQIKAYQSQDQNYADLQNGRLDATLTDKLE 185 TPESL GK VG+ ++ +AYA+ H ++++ YQ+QD+ DL GR+DAT D + Sbjct: 129 TPESLAGKVVGIQASTIHQAYAQEHFK--DSELRVYQTQDEANQDLFAGRIDATQADSI- 185 Query: 186 AQLNFLSKPEGS--DFKTGPAFKDPTLPLDIAMGLRKNDQALRALINKGIAAVQADGTYA 243 A +F+ G + K A + L + G+RK D + A +NKGIAA+ ADGT+A Sbjct: 186 AMADFVGSDAGGCCEIKGAVANDEAILGKGVGAGVRKGDSDVLAALNKGIAAILADGTHA 245 Query: 244 QIQKKYFGDQDIYHE 258 +I KYF IY E Sbjct: 246 EITSKYF-TTSIYSE 259 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: 155 Number of extensions: 9 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: 258 Length of database: 259 Length adjustment: 24 Effective length of query: 234 Effective length of database: 235 Effective search space: 54990 Effective search space used: 54990 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