GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltI in Acidovorax sp. GW101-3H11

Align glutamate-aspartate periplasmic-binding protein (characterized)
to candidate Ac3H11_1603 Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4)

Query= CharProtDB::CH_002441
         (302 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1603
          Length = 305

 Score =  214 bits (546), Expect = 2e-60
 Identities = 121/298 (40%), Positives = 175/298 (58%), Gaps = 17/298 (5%)

Query: 14  ALSAGLAQAD-DAAPAAGST-----LDKIAKNGVIVVGHRESSVPFSY-YDNQQKVVGYS 66
           AL+AGL  A    APA   T     L+KI  +G  V+G RE+S P +Y     +K VGY 
Sbjct: 10  ALAAGLTLACLTTAPALAQTVTQPTLEKIKASGKAVLGVRETSPPMAYALGANEKYVGYH 69

Query: 67  QDYSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNVERQKQAAF 126
            +    +++ +      PD +++ + +T+QN +PL+QNGT D  CG TTNN  RQ+Q AF
Sbjct: 70  VELCERVLKEIA-----PDAKLEYMAVTAQNTLPLVQNGTLDIGCGPTTNNTARQQQVAF 124

Query: 127 SDTIFVVGTRLLTKKGGDIKDFANLKDKAVVVTSGTTSEVLLNKLNEEQKMN---MRIIS 183
           + T +V   R+  +K  D+K    L  + +  ++GTT+  LL K  +E+ +    ++ + 
Sbjct: 125 AVTTYVSEVRMAVRKDSDLKSINQLAGRTIAASTGTTAVQLLRK--QERVLGGAPIKTVL 182

Query: 184 AKDHGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWEIVGKPQSQEAYGCMLRKDDP 243
            KDH +SF  LESGRA AF++DD LLAG  A +K P  + IVG+P   E    + RKDDP
Sbjct: 183 GKDHHESFLLLESGRADAFVLDDNLLAGMIANSKDPSAYRIVGEPLGAEPIALLFRKDDP 242

Query: 244 QFKKLMDDTIAQVQTSGEAEKWFDKWFKNPIPPKNLNMNFELSDEMKALFKEPNDKAL 301
            FK  +D  + ++  SGE EK + KWF NPIPPKN+++N  L   ++ LF  PNDK L
Sbjct: 243 TFKAAVDGVLTKLMQSGEMEKIYTKWFVNPIPPKNMSLNLPLGTTLRQLFATPNDKPL 300


Lambda     K      H
   0.314    0.130    0.366 

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: 196
Number of extensions: 5
Number of successful extensions: 3
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: 302
Length of database: 305
Length adjustment: 27
Effective length of query: 275
Effective length of database: 278
Effective search space:    76450
Effective search space used:    76450
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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