GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo3_N2E3:AO353_15035
          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 (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