GapMind for catabolism of small carbon sources

 

Alignments for a candidate for antC in Pseudomonas putida KT2440

Align electron transfer component of the anthranilate 1,2-dioxygenase system (EC 1.14.12.1) (characterized)
to candidate PP_3163 PP_3163 benzoate 1,2-dioxygenase electron transfer component

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2738
         (343 letters)



>FitnessBrowser__Putida:PP_3163
          Length = 336

 Score =  274 bits (700), Expect = 3e-78
 Identities = 148/337 (43%), Positives = 203/337 (60%), Gaps = 6/337 (1%)

Query: 1   MNHKVAFSFADGKTSFFEVKPNELLLDAALRNGVNIPLDCREGVCGTCQGRCESGRYTQ- 59
           M++++A +F DG T F E    E + DAA R G+NIPLDCR+G CGTC+ + ESGRY   
Sbjct: 1   MSYQIALNFEDGVTRFIEATGQETVADAAYRQGMNIPLDCRDGACGTCKCKAESGRYDLG 60

Query: 60  DYVDDEALSEQDLAQRKMLSCQTRVQSDASFYFDFDSSLCNAGATQLLQAVITGVEQVSA 119
           D   ++ALSE ++A+  +L+CQ R +SD        S LC        +A I+ V Q+S 
Sbjct: 61  DNFIEDALSEDEIAEGYVLTCQMRAESDCVIRIPASSQLCKTEQATF-EAAISDVRQLSV 119

Query: 120 TTAILHLDACSHPRQLDFLPGQYARLHVPGTDEWRSYSFANRPNPDNQLQFLIRLLPDGV 179
           +T  L +   +  R L FLPGQY  L VPG+++ R+YSF++    D ++ FLIR +P G+
Sbjct: 120 STIALSIKGEALSR-LAFLPGQYVNLKVPGSEQSRAYSFSSLQK-DGEVSFLIRNVPGGL 177

Query: 180 MSNFIREHCRPGEVLEFEAPLGSFYLRQVSKPLVLVAGGTGLSAFLGMLDTIAEQGGCGH 239
           MS+F+    + G+ L    PLGSFYLR + +PL+L+AGGTGL+ F  ML+ IAEQG   H
Sbjct: 178 MSSFLTNLAKAGDSLSLAGPLGSFYLRPIQRPLLLLAGGTGLAPFTAMLEKIAEQGS-EH 236

Query: 240 PIQLFYGVTQDNDLCETQRLADYRDKIANFDYHLVVSKPSEHWKGKTGWIPDHFDRQSFE 299
           P+ L YGVT D DL E  RL     +I NF Y   V+ P   +  K G++  H + +   
Sbjct: 237 PLHLIYGVTNDFDLVELDRLQALAARIPNFTYSACVANPDSQYPQK-GYVTQHIEPRHLN 295

Query: 300 ANPFDIYLCGPPPMVEAVKTWFSDQKIERFQMYYEKF 336
               D+YLCGPPPMVEAV  +  +Q I     YYEKF
Sbjct: 296 DGDVDVYLCGPPPMVEAVSQYVREQGITPANFYYEKF 332


Lambda     K      H
   0.322    0.138    0.431 

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: 354
Number of extensions: 17
Number of successful extensions: 6
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: 343
Length of database: 336
Length adjustment: 28
Effective length of query: 315
Effective length of database: 308
Effective search space:    97020
Effective search space used:    97020
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 (21.9 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