GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1750 in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_3314 Dipeptide transport ATP-binding protein DppF (TC 3.A.1.5.2)

Query= TCDB::Q9X272
         (328 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3314
          Length = 326

 Score =  271 bits (692), Expect = 2e-77
 Identities = 135/323 (41%), Positives = 204/323 (63%), Gaps = 8/323 (2%)

Query: 10  MKPLLQTVDLKKYFP------QGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTI 63
           M  +L   DL +++       +G   ++A++G+S E++ G+TL +VGESGCGKSTL R +
Sbjct: 1   MAVVLTARDLTRHYEVSRGMFKGHATVRALNGVSFELEAGKTLAVVGESGCGKSTLARAL 60

Query: 64  LKLLRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLII 123
             +  P  G +   G+++   N  E K  RK +Q++FQ P  SLNP+  +G  + +PL+I
Sbjct: 61  TLIEEPSAGSLKIAGQEVAGANKAERKQLRKDVQMVFQSPYASLNPRQKIGDQLAEPLLI 120

Query: 124 HKIGTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEP 183
           +   +  ERR++V+ ++  VG+  E    +PH FSGGQ+QRI +ARA+ L PK +V DEP
Sbjct: 121 NTKLSATERREKVQAMMKQVGLRPEHYQRYPHMFSGGQRQRIALARAMMLQPKVLVADEP 180

Query: 184 VSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDK 243
            SALDVSIQAQ+++L  ++QQ+   +Y+FI+HNLAVV+H++  V VMYLG+ VE G  + 
Sbjct: 181 TSALDVSIQAQVLNLFMDLQQEFNTAYVFISHNLAVVQHVADDVMVMYLGRPVEMGPNES 240

Query: 244 IFLNPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICF 303
           I+  P+HPYT+ALL + P I  D  K +   + GELP+P++ P GC F  RC      C 
Sbjct: 241 IYSRPLHPYTQALLSATPTIHPDPNKPKI-KIVGELPNPLNPPSGCAFHKRCPYATERCK 299

Query: 304 EKEPELTEVEKNHFVSCHLVRSY 326
            +EP L  ++ N  V+CH    +
Sbjct: 300 TEEPALRPLD-NRLVACHYAERF 321


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: 331
Number of extensions: 12
Number of successful extensions: 2
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: 326
Length adjustment: 28
Effective length of query: 300
Effective length of database: 298
Effective search space:    89400
Effective search space used:    89400
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