Align Arabinose ABC transporter permease (characterized, see rationale)
to candidate GFF2276 PGA1_c23080 ribose transport system permease protein RbsC
Query= uniprot:A0A161GM94 (322 letters) >FitnessBrowser__Phaeo:GFF2276 Length = 324 Score = 169 bits (429), Expect = 6e-47 Identities = 101/300 (33%), Positives = 163/300 (54%), Gaps = 5/300 (1%) Query: 27 LLAAIGIFVL-CTLMIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDLSVGSVIA 85 +L A +F++ T+ FL+ N + + + G+ A + + + SG+ DLSVGS+++ Sbjct: 18 ILIAFALFIIGFTIANPKFLTLDNFENVVRSSAILGVMALGVTFVVISGNLDLSVGSMMS 77 Query: 86 CAGVVAAVVMRDTNSVFLGISAALVMGLIVGLINGIVIAKLRVNALITTLATMQIVRGLA 145 + +V + + D L I A M L +G + G ++ L++N+LI TL + + GL Sbjct: 78 FSTIVV-LDLHDKLGPTLAIPAMFAMTLCLGALIGFLVGYLKLNSLIVTLGMLSAIHGLT 136 Query: 146 YIFANGKAVGVSQES---FFVFGNGQMFGVPVPILITIVCFLFFGWLLNYTTYGRNTMAI 202 ++ GK + ++ + F +FG G + G+ PILI I G +L T +GR A+ Sbjct: 137 LTYSGGKNMDIADKEGTWFAIFGQGNILGIQTPILIFIALAALLGIILAKTPFGRKVYAV 196 Query: 203 GGNQEAALLAGVNVDRTKIIIFAVHGVIGALAGVILASRMTSGQPMIGQGFELTVISACV 262 GGN AA +G+ R + + + + A AG+I ASR Q +GQG EL V++A + Sbjct: 197 GGNGTAATFSGIRRARVVFLCYIMSALCVATAGLIQASRSMGSQNTVGQGLELEVLAAVI 256 Query: 263 LGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLLAVVIDRLKQR 322 LGG SL GG G I + GVLIL I+N + L +D QYV+ I++LAV +D +R Sbjct: 257 LGGASLLGGSGTIFKTVIGVLILGFIQNGLLLVGLDFSVQYVVTWIIIILAVWLDIAAKR 316 Lambda K H 0.330 0.144 0.420 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: 256 Number of extensions: 10 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 322 Length of database: 324 Length adjustment: 28 Effective length of query: 294 Effective length of database: 296 Effective search space: 87024 Effective search space used: 87024 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 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