Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate GFF2519 PGA1_c25580 putative glycine betaine/L-proline transport system permease protein
Query= TCDB::Q9KKE2 (285 letters) >FitnessBrowser__Phaeo:GFF2519 Length = 343 Score = 220 bits (560), Expect = 4e-62 Identities = 114/238 (47%), Positives = 170/238 (71%), Gaps = 8/238 (3%) Query: 43 IEWILRG-------LPWWLVILAFMALACRSSRRWSLTLAVCALLETVGVLGIWDLTMQT 95 + W+L G +PWW++I + ++R+ +T+ V + G++ D+ +QT Sbjct: 93 LSWLLEGALFTFTTIPWWILIPLLVLATWAATRKLGVTIFVAVVFLFFGLIDHLDVALQT 152 Query: 96 LALMLMATIVSVVIGVPMGILVAKSRVVRNITLPVLDVMQTMPSFVYLIPALMLFGLGKV 155 L+++ + T +SV+ GVP+GI++++S ++ I LP+LD++QT+PSFVYLIP + LF + + Sbjct: 153 LSIIFVCTGLSVLFGVPVGIMMSRSDRMQKIMLPILDMLQTLPSFVYLIPLIFLFSVTEP 212 Query: 156 PAI-LATIIYAVPPLIRLTDLGIRQVDAEVVEAATAFGGSPGQILFGVELPLATPTIMAG 214 +A I+YA+ P+IRLTDLGIR VD +VVEAA AFG + Q L+GV+LPLA P IMAG Sbjct: 213 KLYGIAIILYAIVPVIRLTDLGIRLVDKDVVEAADAFGMTDRQKLYGVQLPLALPNIMAG 272 Query: 215 LNQTIMMALSMVVVASMIGARGLGEQVLNGIQTLDVGKGLEAGIGIVILAVVLDRITQ 272 +NQTIMM+L+MVV+AS++ A GLG VL GI+ L++G GL AG GIV+LAVVLDR ++ Sbjct: 273 VNQTIMMSLAMVVIASLVSAPGLGVLVLRGIRNLELGVGLVAGFGIVLLAVVLDRCSK 330 Lambda K H 0.327 0.142 0.422 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: 316 Number of extensions: 11 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: 285 Length of database: 343 Length adjustment: 27 Effective length of query: 258 Effective length of database: 316 Effective search space: 81528 Effective search space used: 81528 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 (21.7 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