GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Azospirillum thiophilum BV-S

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_045582953.1 AL072_RS17755 aldehyde dehydrogenase

Query= metacyc::MONOMER-15108
         (486 letters)



>NCBI__GCF_001305595.1:WP_045582953.1
          Length = 503

 Score =  346 bits (888), Expect = e-100
 Identities = 185/475 (38%), Positives = 279/475 (58%), Gaps = 8/475 (1%)

Query: 15  IDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGP-WKKMTANER 73
           I G+FV    G+   + +P T E    +A+ G  ++D AV AA+ A   P W++MT ++R
Sbjct: 17  IGGRFVEPKSGRYIPSYDPTTAEPWYELADAGPEDVDDAVAAARAAFVDPAWRRMTQSDR 76

Query: 74  IAVLRKVGDLILERKEELSVLESLDTGK--PTWLSGSIDIPRAAYNFHFFSDYIRTITNE 131
             ++R++ +LIL   EEL+++E+ D GK      +    +P +   F   +D ++  T  
Sbjct: 77  GKLVRRLAELILVNAEELALMETRDNGKLIKEMRAQMRAMPDSYTYFAGMADKLQGDTIP 136

Query: 132 ATQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTAT 191
             ++D   LN+ +R P+GV+G+I PWN PL+L+T  LAP LA GNTVV+KP+E    +  
Sbjct: 137 VNKLD--MLNFNLREPLGVVGMITPWNSPLMLLTGTLAPCLAIGNTVVIKPSEHATASTL 194

Query: 192 VLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTL 251
            LAE+  +AG P GVVN+V G G  +AG ALT HP +  I FTG T TG  I A+AA  L
Sbjct: 195 ALAELVAEAGFPAGVVNVVSGAGA-TAGEALTRHPGIAKIVFTGSTQTGSRIAANAAGNL 253

Query: 252 KRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKF 311
                ELGGK+P+V+F D +++  +   +   F   G+ C+ GSR +VE   Y+ F+E  
Sbjct: 254 VPCQMELGGKSPHVVFGDVDIERAVNGVVAGVFAAAGQTCVAGSRCFVEASIYDRFVEAL 313

Query: 312 VAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPE--GLEKG 369
           VA+T  + VG P +  T +G L       +V  Y+     +G  +  GG+RP+  GL++G
Sbjct: 314 VARTGRIAVGHPMEEGTDIGPLALSPQLAKVEEYVASGQRDGARLAAGGRRPQAAGLDRG 373

Query: 370 YFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRR 429
           ++ EPT++     D   +++EIFGPVV V+PF +E+E++   NDT YGL++ +WT D+ R
Sbjct: 374 WYFEPTVLADARNDMGFMRDEIFGPVVGVVPFASEDEMIAMANDTRYGLASGIWTGDIDR 433

Query: 430 AHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICI 484
           A R A +I+AG VW+NT+      +  GG KQSG GR GG      +S   N+ I
Sbjct: 434 AMRFATRIDAGTVWINTYRAAAYMSSNGGFKQSGYGRRGGFDVMREFSRSKNVVI 488


Lambda     K      H
   0.318    0.136    0.404 

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: 622
Number of extensions: 32
Number of successful extensions: 5
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: 486
Length of database: 503
Length adjustment: 34
Effective length of query: 452
Effective length of database: 469
Effective search space:   211988
Effective search space used:   211988
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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