GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Pseudomonas fluorescens FW300-N2E3

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate AO353_06035 AO353_06035 amino acid ABC transporter permease/ATP-binding protein

Query= TCDB::P73650
         (240 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_06035
          Length = 512

 Score =  116 bits (290), Expect = 1e-30
 Identities = 67/214 (31%), Positives = 121/214 (56%), Gaps = 8/214 (3%)

Query: 20  ILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLG---SDQ 76
           +L+GI+ ++  G+++++IGP+G+GK++L +TI GL +  QGEI+  GE+  G     +  
Sbjct: 275 VLKGIDLTVGSGQVISIIGPSGSGKTSLIRTINGLESIDQGEIMLFGESFIGSNDTPNSA 334

Query: 77  IVRRGMCYVPQVC---NVFGSLTVAENLDMGAFLHQGPTQTLKDRIYTMFPK--LAQRRN 131
            VR G+ ++  V    N+F    + +N+ +    H       + R Y +  K  L    +
Sbjct: 335 KVRSGVRHIGMVFQNFNLFPHRCILDNITLAPRFHGSAKPLSEQRAYALLDKVGLLAHAH 394

Query: 132 QRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAINATGKAIIL 191
           +    LSGG++Q +A+ RAL ++P ++L DEP++AL P LV DV   I+ +   G  +++
Sbjct: 395 KYPHQLSGGQQQRVAIARALAMEPKIMLFDEPTSALDPELVGDVLNVIRDLAKEGMTMLI 454

Query: 192 VEQNAKQALMMADRGYVLENGRDKLEGSGQSLLN 225
           V      A+ ++DR   +ENG  +L+ S  ++ N
Sbjct: 455 VTHEMDFAMSISDRVIFMENGNVQLDASPYAIRN 488


Lambda     K      H
   0.320    0.139    0.393 

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: 226
Number of extensions: 11
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: 240
Length of database: 512
Length adjustment: 29
Effective length of query: 211
Effective length of database: 483
Effective search space:   101913
Effective search space used:   101913
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:

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