Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate SMc02738 SMc02738 glycine betaine transport system permease ABC transporter protein
Query= TCDB::Q9KKE2 (285 letters) >FitnessBrowser__Smeli:SMc02738 Length = 281 Score = 221 bits (564), Expect = 1e-62 Identities = 120/263 (45%), Positives = 170/263 (64%) Query: 8 LSIRAPVNDFIQALVTNYGWVFKAISGVILKAVLFIEWILRGLPWWLVILAFMALACRSS 67 + I A F+ L TN+ F ++ V+ + + +IL+ ++I ALA Sbjct: 9 IPIGAWAKSFVDWLTTNFNLFFDQLANVLSAIISVLLYILQTPHPLIIIAVVTALAWWFR 68 Query: 68 RRWSLTLAVCALLETVGVLGIWDLTMQTLALMLMATIVSVVIGVPMGILVAKSRVVRNIT 127 R + C L + G W T +TLAL+L AT VS+ +GVP GI A+ + +I Sbjct: 69 RSLGIAAFTCLGLLLIVNQGYWQETTETLALVLAATFVSMAVGVPFGIAAARRAWIYSIM 128 Query: 128 LPVLDVMQTMPSFVYLIPALMLFGLGKVPAILATIIYAVPPLIRLTDLGIRQVDAEVVEA 187 P+LD+MQT+P+FVYLIPAL+LFGLG VP ++AT+I+A+P IRLT LGI +VEA Sbjct: 129 RPILDLMQTIPTFVYLIPALILFGLGVVPGLIATVIFAIPAPIRLTRLGIISTPPALVEA 188 Query: 188 ATAFGGSPGQILFGVELPLATPTIMAGLNQTIMMALSMVVVASMIGARGLGEQVLNGIQT 247 A +FG +P Q+L VELP A P IMAGL QTIM++LSMVV+A+++GA GLG VL + T Sbjct: 189 AESFGATPWQVLRKVELPFAMPQIMAGLTQTIMLSLSMVVIAALVGADGLGVPVLRALNT 248 Query: 248 LDVGKGLEAGIGIVILAVVLDRI 270 +++ +G E+G+ IVILA+VLDR+ Sbjct: 249 VNIARGFESGLCIVILAIVLDRL 271 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: 273 Number of extensions: 15 Number of successful extensions: 1 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: 281 Length adjustment: 26 Effective length of query: 259 Effective length of database: 255 Effective search space: 66045 Effective search space used: 66045 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: 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