GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Pseudomonas stutzeri RCH2

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate GFF4232 Psest_4305 NAD-dependent aldehyde dehydrogenases

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



>FitnessBrowser__psRCH2:GFF4232
          Length = 497

 Score =  368 bits (944), Expect = e-106
 Identities = 203/476 (42%), Positives = 285/476 (59%), Gaps = 4/476 (0%)

Query: 14  FIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALN-GPWKKMTANE 72
           FI G++  + DG  FD I+P     L  VA    A+ + AV +A+ A + G W ++   +
Sbjct: 23  FIQGEYCAAADGGQFDCISPVDGRVLAQVASCEQADAERAVASARAAFDAGSWSRLAPAK 82

Query: 73  RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132
           R AVL +  DL+   +EEL++LE+LD GKP   S ++DIP AA    +  + I  I +E 
Sbjct: 83  RKAVLIRFADLLEANREELALLETLDMGKPIGDSLAVDIPGAARALRWSGEAIDKIYDEV 142

Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192
                  L    R PVGV+  I PWN PL++  WKL PALA GN+VV+KP+E +P+TA  
Sbjct: 143 AATPHDQLGLVTREPVGVVAAIVPWNFPLMMACWKLGPALATGNSVVLKPSEKSPLTAIR 202

Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKT-L 251
           +A++  DAG+P GV+N++ G+G ++ G AL  H DV+ + FTG T   K +M  A ++ +
Sbjct: 203 IAQLAIDAGIPAGVLNVLPGYG-HTVGKALALHMDVDTLVFTGSTRVAKQLMIYAGESNM 261

Query: 252 KRLSYELGGKNPNVIFADS-NLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEK 310
           KR+  E GGK+PN++FAD+ +L    +    +   NQGEVC  GSR+ VER   E FL  
Sbjct: 262 KRVWLEAGGKSPNIVFADAPDLQAAAQAAAGAIAFNQGEVCTAGSRLLVERSIRERFLPM 321

Query: 311 FVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGY 370
            V   K    G+P D  T VGAL+  +    V GYI    + G  +L GG+R      G 
Sbjct: 322 VVEALKGWKPGNPLDPATNVGALVDTQQLNTVLGYIDAGRQAGAQVLIGGQRTLEETGGL 381

Query: 371 FLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRA 430
           ++EPTI  G+    R+ +EEIFGPV++VI FD+ EE +   NDT YGL+A+VWT DL +A
Sbjct: 382 YVEPTIFDGVDNAMRIAQEEIFGPVLSVITFDSAEEAVAIANDTPYGLAAAVWTADLSKA 441

Query: 431 HRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIKL 486
           HR A  + AG VWVN +   D+  PFGG KQSG GR+  LH+F+ Y+EL    I+L
Sbjct: 442 HRTARALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTELKATWIQL 497


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: 630
Number of extensions: 20
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: 497
Length adjustment: 34
Effective length of query: 452
Effective length of database: 463
Effective search space:   209276
Effective search space used:   209276
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 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