GapMind for catabolism of small carbon sources

 

Aligments for a candidate for TM0028 in Pseudomonas fluorescens FW300-N2E2

Align TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate Pf6N2E2_3314 Dipeptide transport ATP-binding protein DppF (TC 3.A.1.5.2)

Query= TCDB::Q9WXN5
         (330 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3314 Dipeptide transport
           ATP-binding protein DppF (TC 3.A.1.5.2)
          Length = 326

 Score =  197 bits (502), Expect = 2e-55
 Identities = 119/328 (36%), Positives = 194/328 (59%), Gaps = 24/328 (7%)

Query: 4   ILLKAENVRAYYKLEK------VSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFM 57
           ++L A ++  +Y++ +       +V+A++G+SFE+   + + VVGESGCGK+TL+     
Sbjct: 3   VVLTARDLTRHYEVSRGMFKGHATVRALNGVSFELEAGKTLAVVGESGCGKSTLA----- 57

Query: 58  NMVKPLTLVDGKIF--LRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRM 115
              + LTL++      L++ G+ V  ++    + +RK   K++ ++ Q+   +L P  ++
Sbjct: 58  ---RALTLIEEPSAGSLKIAGQEVAGAN----KAERKQLRKDVQMVFQSPYASLNPRQKI 110

Query: 116 -EKYVRHLAESHGIDEEELLDKARRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIATIL 174
            ++    L  +  +   E  +K +   ++VGL P   +RYP   SGG RQR  +A A +L
Sbjct: 111 GDQLAEPLLINTKLSATERREKVQAMMKQVGLRPEHYQRYPHMFSGGQRQRIALARAMML 170

Query: 175 NPSLLIADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYA 234
            P +L+ADEPTSALDV  Q  +L + M + +Q    + +FI+H++A V+ +AD +++MY 
Sbjct: 171 QPKVLVADEPTSALDVSIQAQVLNLFMDL-QQEFNTAYVFISHNLAVVQHVADDVMVMYL 229

Query: 235 GKIVEFAPVESLLEKPLHPYTQGLFNSVLTPEPEVKKRGITTIPGAPPNLINPPSGCRFH 294
           G+ VE  P ES+  +PLHPYTQ L ++  T  P+  K  I  I G  PN +NPPSGC FH
Sbjct: 230 GRPVEMGPNESIYSRPLHPYTQALLSATPTIHPDPNKPKI-KIVGELPNPLNPPSGCAFH 288

Query: 295 PRCPHAMDVCKEKEPPLTEIEPGRRVAC 322
            RCP+A + CK +EP L  ++  R VAC
Sbjct: 289 KRCPYATERCKTEEPALRPLD-NRLVAC 315


Lambda     K      H
   0.321    0.138    0.405 

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: 290
Number of extensions: 10
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: 330
Length of database: 326
Length adjustment: 28
Effective length of query: 302
Effective length of database: 298
Effective search space:    89996
Effective search space used:    89996
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.

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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 paper from 2022 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