GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1749 in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_3313 Dipeptide transport ATP-binding protein DppD (TC 3.A.1.5.2)

Query= TCDB::Q9X271
         (324 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3313
          Length = 322

 Score =  269 bits (687), Expect = 8e-77
 Identities = 145/304 (47%), Positives = 189/304 (62%), Gaps = 1/304 (0%)

Query: 2   MELLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRN 61
           M LL + NL V F      V  VDG+   + KGE L IVGESGSGKSV++++L+ LI   
Sbjct: 1   MSLLEIKNLNVRFGDATA-VPVVDGLDLTVEKGEVLAIVGESGSGKSVTMMALMGLIEHP 59

Query: 62  GRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHR 121
           G +      F GK++LKL+  + R I GKD++++FQ+PMT+LNP   VG Q+ E +  H 
Sbjct: 60  GIVTADALNFDGKNMLKLSNRQRRQIVGKDLAMVFQDPMTALNPSYTVGFQIEEVLRLHL 119

Query: 122 LMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEP 181
            M  + AR+RAIELLE+V IP +  R   YP Q SGGM QRV IAMA+A  PKLLIADEP
Sbjct: 120 KMSGKAARKRAIELLEKVEIPGAASRMDAYPHQLSGGMSQRVAIAMAIAGEPKLLIADEP 179

Query: 182 TTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEE 241
           TTALDVTIQAQIM+LL  L++E  M ++ ITHDL+V      R+  MYAG+ VE   V E
Sbjct: 180 TTALDVTIQAQIMDLLLALQKEQNMGLVLITHDLAVVAETAQRVCVMYAGQAVEVGKVPE 239

Query: 242 ILKTPLHPYTKGLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQRE 301
           +   P HPY++ LL +  E      +L  +PG  P     P GC   PRC +  + C+ +
Sbjct: 240 LFDIPAHPYSEALLAAIPEHSMGAARLATLPGIVPGRYDRPQGCLLSPRCPYVQDNCRVQ 299

Query: 302 EPPL 305
            P L
Sbjct: 300 RPAL 303


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: 257
Number of extensions: 14
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: 324
Length of database: 322
Length adjustment: 28
Effective length of query: 296
Effective length of database: 294
Effective search space:    87024
Effective search space used:    87024
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.

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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