GapMind for catabolism of small carbon sources

 

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

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate AO353_15035 AO353_15035 aldehyde dehydrogenase

Query= BRENDA::Q4DRT8
         (561 letters)



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

 Score =  135 bits (339), Expect = 5e-36
 Identities = 129/438 (29%), Positives = 194/438 (44%), Gaps = 32/438 (7%)

Query: 92  IDTALQASRE------WSQTSFRDRAAIFLHAAHLISTKYRHELRAATMLGQSKSPFQAE 145
           +D A+ ++R+      WS  S  +R  + L  A LI    R EL     L   K    A 
Sbjct: 57  VDAAVISARQAFESGVWSARSPGERKQVLLRLAELIMAN-REELALLDSLNMGKPVMDAY 115

Query: 146 IDVIAESCDFLRFSVHYAENLYRDQPLSPSSGAVWNSLDYRPLEGFVSTIAPFNFAAIAA 205
              +  +    R+     + LY DQ ++PS+  V  ++    L G V+ + P+NF    A
Sbjct: 116 TIDVPGAAGVFRWYAESLDKLY-DQ-IAPSAQNVLATITREAL-GVVAAVVPWNFPLDMA 172

Query: 206 NLVACPALM-GNVVLWKPSPHAVLSNYLLYKVFEEAGLPAGVVNFLPCEPDVMTNFVNSH 264
                PAL  GN V+ KP+  +  S   L ++  EAG+P GV+N LP   +     +  H
Sbjct: 173 AWKLAPALAAGNSVILKPAEQSPFSALRLGELALEAGVPPGVLNVLPGLGEQAGKALGLH 232

Query: 265 RDLAGVAFTGSTKVFMSINKQIYARLEEYRNIPRISGETGGKDFHLVHPSA-DLKLAAAL 323
            D+  + FTGST+V      + + +     N+ ++  E GGK  +LV     DL LAA  
Sbjct: 233 LDIDCLVFTGSTEV-----GKYFMQYSAQSNLKQVWLECGGKSANLVFADCQDLDLAAQK 287

Query: 324 TVRGAFEFQGQKCSATSRLYAPKSRWEELKNYMLGVHEQLKMGQPDDFKSFMCAVIDETA 383
              G F  QG+ CSA SRL   +S  +E    ++   E+ + G P D  S   A++D   
Sbjct: 288 AAFGIFFNQGEVCSANSRLLVERSIHDEFVERLMVQVERWQPGDPLDSSSTAGAIVDSRQ 347

Query: 384 FERNKKYIDIAKSSPSTYSVIAGGGYDKTEGW--FVQPTIVESKDSQAQLMHEEIFGPIL 441
             R  K+I  A+   +    + GG      G   F+QPTI     +   L  +E+FGP+L
Sbjct: 348 TARIMKFIQQAERQGA--KRVCGGQQSIINGSDNFIQPTIFTGVTADMPLFRDEVFGPVL 405

Query: 442 TVHVYDDSKPGFWSDVCDVVNRSTKYALTGSIFAQDRQAIRDATTKHLRYAAGNYYINDK 501
            V  +DD      +    + N S  Y L  S++  D         + LR  AG   +N  
Sbjct: 406 AVTAFDDE-----ASALQLANDSV-YGLAASLWTDDLNRAH-RVARQLR--AGTVSVNS- 455

Query: 502 CTGAVVGQQPFGGARASG 519
              A+    PFGG + SG
Sbjct: 456 -VDALDVTVPFGGGKQSG 472


Lambda     K      H
   0.320    0.133    0.402 

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: 596
Number of extensions: 25
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: 561
Length of database: 496
Length adjustment: 35
Effective length of query: 526
Effective length of database: 461
Effective search space:   242486
Effective search space used:   242486
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 (21.8 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