GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Pseudomonas fluorescens FW300-N2E3

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate AO353_15035 AO353_15035 aldehyde dehydrogenase

Query= BRENDA::P23883
         (495 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_15035
          Length = 496

 Score =  508 bits (1308), Expect = e-148
 Identities = 255/492 (51%), Positives = 339/492 (68%), Gaps = 4/492 (0%)

Query: 6   LAYWQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSA 65
           L YWQ +A +L    +  I G+   A   +TF  ++P T A LA++A   + D+D A+ +
Sbjct: 4   LEYWQGQAAALQFPTQALIEGKQRPAQSGQTFAAINPATGAVLAEVAACGNADVDAAVIS 63

Query: 66  ARGVFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAA 125
           AR  FE G WS  SP +RK VL +LA+L+ A+ EELALL++L+ GKP+  +   D+PGAA
Sbjct: 64  ARQAFESGVWSARSPGERKQVLLRLAELIMANREELALLDSLNMGKPVMDAYTIDVPGAA 123

Query: 126 RAIRWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAG 185
              RWYAE++DK+Y ++A ++ + LA I RE +GV+AA+VPWNFPL +  WKL PALAAG
Sbjct: 124 GVFRWYAESLDKLYDQIAPSAQNVLATITREALGVVAAVVPWNFPLDMAAWKLAPALAAG 183

Query: 186 NSVILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGS 245
           NSVILKP+E+SP SA+RL  LA EAG+P GVLNV+ G G +AG+AL  H DID + FTGS
Sbjct: 184 NSVILKPAEQSPFSALRLGELALEAGVPPGVLNVLPGLGEQAGKALGLHLDIDCLVFTGS 243

Query: 246 TRTGKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAG 305
           T  GK  ++ +  SN+K+VWLE GGKSAN+VFADC DL  AA   A GIF+NQG+VC A 
Sbjct: 244 TEVGKYFMQYSAQSNLKQVWLECGGKSANLVFADCQDLDLAAQKAAFGIFFNQGEVCSAN 303

Query: 306 TRLLLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQ 365
           +RLL+E SI DEF+  L  Q + WQPG PLD ++T G ++D      +  FI++ E +G 
Sbjct: 304 SRLLVERSIHDEFVERLMVQVERWQPGDPLDSSSTAGAIVDSRQTARIMKFIQQAERQGA 363

Query: 366 LLLDGRNAGLAAA----IGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDS 421
             + G    +       I PTIF  V  +  L R+E+FGPVL VT F  E  ALQLANDS
Sbjct: 364 KRVCGGQQSIINGSDNFIQPTIFTGVTADMPLFRDEVFGPVLAVTAFDDEASALQLANDS 423

Query: 422 QYGLGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALE 481
            YGL A++WT DL+RAHR++R+L+AG+V VN+ +  D+TVPFGG KQSG GRD SLH+ +
Sbjct: 424 VYGLAASLWTDDLNRAHRVARQLRAGTVSVNSVDALDVTVPFGGGKQSGFGRDLSLHSFD 483

Query: 482 KFTELKTIWISL 493
           K+T+LKT W  L
Sbjct: 484 KYTQLKTTWFQL 495


Lambda     K      H
   0.317    0.133    0.389 

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: 609
Number of extensions: 21
Number of successful extensions: 2
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: 495
Length of database: 496
Length adjustment: 34
Effective length of query: 461
Effective length of database: 462
Effective search space:   212982
Effective search space used:   212982
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