GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1749 in Pseudomonas fluorescens FW300-N1B4

Align TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate Pf1N1B4_5105 Peptide ABC transporter, ATP-binding protein

Query= TCDB::Q9X271
         (324 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5105
          Length = 323

 Score =  224 bits (571), Expect = 2e-63
 Identities = 130/312 (41%), Positives = 182/312 (58%), Gaps = 16/312 (5%)

Query: 2   MELLNVNNLKVEFHR----VEGI----VKAVDGISYKLNKGESLGIVGESGSGKSVSVLS 53
           M LL V +L V F      + G+    + AV+G+S  L+ GE+LG+VGESGSGKS    S
Sbjct: 1   MTLLKVKDLHVRFAAPGTGLMGMNRQWLTAVNGVSLTLSAGETLGLVGESGSGKS----S 56

Query: 54  LLRLINRNGRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQV 113
           L R I     I  G+ +F G D+    K ++  +R  + +++FQ+P  +LNP + +G  +
Sbjct: 57  LGRAILHLNEIYAGQVLFDGIDMAHAGKVDITRLR-HETAMVFQDPYAALNPRLSIGQTL 115

Query: 114 MEPIIWHRLMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHP 173
            E +   R +       R  ELL  VG+   P+     P   SGG  QRV IA ALA  P
Sbjct: 116 AEVLRVQRKVPESLIAARVGELLTLVGL--RPELASRKPHALSGGQCQRVGIARALAVEP 173

Query: 174 KLLIADEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKI 233
           +L++ADE   ALDV+IQ QI+ LL EL++   ++++FI HDL++    CDR+  MY GKI
Sbjct: 174 RLIVADECVAALDVSIQGQIINLLLELRQRMNLAIVFIAHDLAIVRRLCDRVAVMYLGKI 233

Query: 234 VEEAPVEEILKTPLHPYTKGLLNSTLEIG-SRGKKLVPIPGNPPNPTKHPSGCKFHPRCS 292
           VEE PVEE+ ++P HPYT  L+ S  EI  +R     P+PG PP+P + PSGC FHPRC 
Sbjct: 234 VEEGPVEEVFRSPRHPYTAALIQSIPEIDPARALPTDPLPGEPPSPLQLPSGCAFHPRCR 293

Query: 293 FAMEICQREEPP 304
           +    C +  PP
Sbjct: 294 YVRATCSQVVPP 305


Lambda     K      H
   0.320    0.139    0.401 

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: 265
Number of extensions: 13
Number of successful extensions: 4
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: 324
Length of database: 323
Length adjustment: 28
Effective length of query: 296
Effective length of database: 295
Effective search space:    87320
Effective search space used:    87320
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: 48 (23.1 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