GapMind for catabolism of small carbon sources

 

Aligments for a candidate for TM1749 in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_5057 Dipeptide transport ATP-binding protein DppD (TC 3.A.1.5.2)

Query= TCDB::Q9X271
         (324 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5057 Dipeptide
           transport ATP-binding protein DppD (TC 3.A.1.5.2)
          Length = 322

 Score =  272 bits (695), Expect = 9e-78
 Identities = 145/304 (47%), Positives = 192/304 (63%), Gaps = 1/304 (0%)

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

Query: 62  GRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHR 121
           G +      F GK++LKLN  + R I GKD+S++FQ+PMT+LNP   VG Q+ E +  H 
Sbjct: 60  GIVTADALNFDGKNMLKLNNRQRRQIVGKDLSMVFQDPMTALNPSYTVGFQIEEVLRLHL 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 +
Sbjct: 180 TTALDVTIQAQIMDLLLALQKEQNMGLVLITHDLAVVAETAQRVCVMYAGQAVEVGQVPQ 239

Query: 242 ILKTPLHPYTKGLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQRE 301
           +   P HPY++ LL +  E      +L  +PG  P     P GC   PRC +  + C+++
Sbjct: 240 LFDIPAHPYSEALLKAIPEHSLGASRLSTLPGIVPGRYDRPQGCLLSPRCPYVKDNCRQQ 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: 260
Number of extensions: 12
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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