GapMind for catabolism of small carbon sources

 

Aligments for a candidate for praB in Pseudomonas fluorescens FW300-N2E3

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate AO353_15035 AO353_15035 aldehyde dehydrogenase

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



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_15035 AO353_15035 aldehyde
           dehydrogenase
          Length = 496

 Score =  357 bits (917), Expect = e-103
 Identities = 195/475 (41%), Positives = 289/475 (60%), Gaps = 4/475 (0%)

Query: 15  IDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKAL-NGPWKKMTANER 73
           I+GK  P+  G+TF  INPAT   L  VA  G A++D AV +A++A  +G W   +  ER
Sbjct: 22  IEGKQRPAQSGQTFAAINPATGAVLAEVAACGNADVDAAVISARQAFESGVWSARSPGER 81

Query: 74  IAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEAT 133
             VL ++ +LI+  +EEL++L+SL+ GKP   + +ID+P AA  F ++++ +  + ++  
Sbjct: 82  KQVLLRLAELIMANREELALLDSLNMGKPVMDAYTIDVPGAAGVFRWYAESLDKLYDQIA 141

Query: 134 QMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVL 193
                 L    R  +GV+  + PWN PL +  WKLAPALAAGN+V++KPAE +P +A  L
Sbjct: 142 PSAQNVLATITREALGVVAAVVPWNFPLDMAAWKLAPALAAGNSVILKPAEQSPFSALRL 201

Query: 194 AEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMA-SAAKTLK 252
            E+  +AGVP GV+N++ G G   AG AL  H D++ + FTG T  GK  M  SA   LK
Sbjct: 202 GELALEAGVPPGVLNVLPGLG-EQAGKALGLHLDIDCLVFTGSTEVGKYFMQYSAQSNLK 260

Query: 253 RLSYELGGKNPNVIFAD-SNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKF 311
           ++  E GGK+ N++FAD  +LD   +      F NQGEVC   SR+ VER  ++ F+E+ 
Sbjct: 261 QVWLECGGKSANLVFADCQDLDLAAQKAAFGIFFNQGEVCSANSRLLVERSIHDEFVERL 320

Query: 312 VAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYF 371
           + + +    GDP D+ +  GA++      R+  +I+ A  +G   + GG++        F
Sbjct: 321 MVQVERWQPGDPLDSSSTAGAIVDSRQTARIMKFIQQAERQGAKRVCGGQQSIINGSDNF 380

Query: 372 LEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAH 431
           ++PTI TG+T D  + ++E+FGPV+ V  FD E   L+  ND+ YGL+AS+WT+DL RAH
Sbjct: 381 IQPTIFTGVTADMPLFRDEVFGPVLAVTAFDDEASALQLANDSVYGLAASLWTDDLNRAH 440

Query: 432 RVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIKL 486
           RVA Q+ AG V VN+    D+  PFGG KQSG GR+  LHSF+ Y++L     +L
Sbjct: 441 RVARQLRAGTVSVNSVDALDVTVPFGGGKQSGFGRDLSLHSFDKYTQLKTTWFQL 495


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: 549
Number of extensions: 20
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: 486
Length of database: 496
Length adjustment: 34
Effective length of query: 452
Effective length of database: 462
Effective search space:   208824
Effective search space used:   208824
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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