Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate PP_2774 PP_2774 glycine betaine ABC transporter, ATPase/permease fusion protein
Query= TCDB::Q9KKE2 (285 letters) >FitnessBrowser__Putida:PP_2774 Length = 698 Score = 212 bits (540), Expect = 2e-59 Identities = 115/262 (43%), Positives = 171/262 (65%), Gaps = 11/262 (4%) Query: 18 IQALVTNYGWVFKAISGVILKAVLFIEWILRG-------LPWWLVILAFMALACRSSRRW 70 I AL+ GW + ++ + ++ G +PW + LA + LA RS+ Sbjct: 429 IDALI---GWSQVTFESAFVGVIVAVRTVINGVEGALGWIPWPVPALALVYLAWRSAGA- 484 Query: 71 SLTLAVCALLETVGVLGIWDLTMQTLALMLMATIVSVVIGVPMGILVAKSRVVRNITLPV 130 L L L +G+ G W+ T+ T+AL+ + ++S++IG+P GIL+AK + R + P+ Sbjct: 485 ILALTTALALGYIGLFGFWERTISTIALVGASVLLSLLIGIPTGILLAKRALARRLVTPL 544 Query: 131 LDVMQTMPSFVYLIPALMLFGLGKVPAILATIIYAVPPLIRLTDLGIRQVDAEVVEAATA 190 LDVMQT+P+FVYLIPA+ F +GK PA++AT+I+A+ P+IRLT LGI++V VEAA A Sbjct: 545 LDVMQTLPTFVYLIPAVAFFSVGKTPAVIATVIFALAPMIRLTALGIQEVPKAAVEAAVA 604 Query: 191 FGGSPGQILFGVELPLATPTIMAGLNQTIMMALSMVVVASMIGARGLGEQVLNGIQTLDV 250 G +P Q L VELPLA+ +++ G+NQTI+M+LSMVVVA++IGA GLG V+ ++ + Sbjct: 605 HGATPWQTLTRVELPLASGSLLLGVNQTIVMSLSMVVVAALIGAGGLGYDVMTALRNIKG 664 Query: 251 GKGLEAGIGIVILAVVLDRITQ 272 G+G+ AGI IV A+V DRI Q Sbjct: 665 GEGVLAGIAIVFCALVPDRIIQ 686 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: 414 Number of extensions: 16 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: 698 Length adjustment: 32 Effective length of query: 253 Effective length of database: 666 Effective search space: 168498 Effective search space used: 168498 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: 51 (24.3 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