GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1750 in Pseudomonas fluorescens FW300-N2C3

Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate AO356_29390 AO356_29390 ABC transporter ATP-binding protein

Query= TCDB::Q9X272
         (328 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_29390
          Length = 329

 Score =  276 bits (707), Expect = 4e-79
 Identities = 150/310 (48%), Positives = 203/310 (65%), Gaps = 17/310 (5%)

Query: 19  LKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGGKIFFEG 78
           + K F +   ILKAVDG+S+ +  GETLGLVGESGCGKSTL + +L LL P  G +   G
Sbjct: 18  INKGFFKPAAILKAVDGVSLRLMRGETLGLVGESGCGKSTLAKLLLGLLAPTSGDVLVNG 77

Query: 79  KDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKRVEE 138
           K +   + KEM    + +Q IFQDP  SLNP+ T+  II  PLI+H IG+  ERRK+ E 
Sbjct: 78  KHLAATDRKEMA---RHIQPIFQDPYSSLNPRKTLRDIITLPLIVHDIGSPAERRKKTEA 134

Query: 139 LLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDL 198
           +LD+VG+ +  I+S+P + SGGQ+QR+ IARAL + P  ++CDEP SALDVS+QAQI++L
Sbjct: 135 MLDVVGLPKRVIDSYPSQLSGGQRQRVAIARALIMRPDVLICDEPTSALDVSVQAQILNL 194

Query: 199 LEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRALLK 258
           L++++++ G++YL I+HNLAV+EH++ +VAVMYLG+IVE    + +F  P HPYTRALL 
Sbjct: 195 LQDLKREFGLTYLLISHNLAVIEHLADRVAVMYLGRIVEERTRESLFAEPGHPYTRALLD 254

Query: 259 SV----PK--IPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPELTEV 312
           SV    P+  IP  G       L G  P+P+  P GC F  RC    A C    P    +
Sbjct: 255 SVLTPDPRLGIPEIG-------LHGTFPNPMSPPSGCAFHPRCPSCFAPCKTAYPANDPI 307

Query: 313 EKNHFVSCHL 322
              + V CHL
Sbjct: 308 IGGN-VRCHL 316


Lambda     K      H
   0.321    0.142    0.417 

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: 323
Number of extensions: 9
Number of successful extensions: 3
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: 328
Length of database: 329
Length adjustment: 28
Effective length of query: 300
Effective length of database: 301
Effective search space:    90300
Effective search space used:    90300
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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