Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate Pf6N2E2_1098 Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein
Query= uniprot:A0A1N7UK26 (258 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1098 Length = 260 Score = 193 bits (491), Expect = 3e-54 Identities = 96/234 (41%), Positives = 148/234 (63%), Gaps = 4/234 (1%) Query: 27 IRFGVFPEYPPFESVAADGSLQGFDIELGNAICAKLEVKCTWVHNEFDGMIPALRARKFD 86 +R G+ YPPF S D ++ GFD ++G A+CA+++V+C W EFDG+IPAL+ +K D Sbjct: 29 LRIGIEAAYPPFASKTPDNAIVGFDYDIGQALCAEMKVRCVWQEQEFDGLIPALKVKKVD 88 Query: 87 AIMSSMAVTPAREKIIDFSDRLFLSPTSVITRKSADFGDTPESLMGKQVGVLQGSLQEAY 146 A++SSM++TP R K +DF+DR + P ++ RK + D P L GK++GV + + + Y Sbjct: 89 AVISSMSITPERLKSVDFTDRYYRIPARLVFRKGSGINDIPAQLNGKRIGVQRATNFDRY 148 Query: 147 ARAHLAKLGAQIKAYQSQDQNYADLQNGRLDATLTDKLEAQLNFLSKPEGSDFK-TGPAF 205 H A GA++ Y SQ++ + DL GRLDAT+ + + L +PEG+DF+ GP F Sbjct: 149 VTDHFAPAGAEVVRYGSQNEIFLDLLGGRLDATMASSVVIDESLLKRPEGNDFEFVGPNF 208 Query: 206 -KDPTLPLDIAMGLRKNDQALRALINKGIAAVQADGTYAQIQKKYFGDQDIYHE 258 ++ I + +RKND L N+ +A ++A+GTY +I++KYF D DIY E Sbjct: 209 TEEQYFGTGIGIAVRKND-TLAGRFNQALATIRANGTYERIRQKYF-DFDIYGE 260 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: 187 Number of extensions: 12 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: 260 Length adjustment: 24 Effective length of query: 234 Effective length of database: 236 Effective search space: 55224 Effective search space used: 55224 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