GapMind for catabolism of small carbon sources

 

Aligments 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_29295 AO353_29295 aldehyde dehydrogenase

Query= BRENDA::P23883
         (495 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_29295 AO353_29295 aldehyde
           dehydrogenase
          Length = 496

 Score =  542 bits (1397), Expect = e-159
 Identities = 275/489 (56%), Positives = 345/489 (70%), Gaps = 4/489 (0%)

Query: 9   WQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARG 68
           W+    SL IE R FI+G Y +A   +TFE V PV    LA +A     D + A+  AR 
Sbjct: 8   WEQHFQSLTIEGRAFIDGHYCSALSRDTFECVSPVDGRFLANVASTDEADANAAVQVARR 67

Query: 69  VFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAI 128
            F+ G W+  +PA+RK +L + ADL+ A+ EELALLETLD GKPI  S+  DIP  A AI
Sbjct: 68  AFDSGVWAKLAPAERKRILIRFADLILANQEELALLETLDMGKPISDSMAIDIPATANAI 127

Query: 129 RWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSV 188
           RW AEAIDK+Y EVA T   +L ++ REP GV+AAIVPWNFPL++  WK  PALAAGNS 
Sbjct: 128 RWSAEAIDKIYDEVAATPHDQLGLVTREPSGVVAAIVPWNFPLIMASWKFAPALAAGNSF 187

Query: 189 ILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRT 248
           ILKPSEKSPL+AIR+A LA +AG+P GV NV+ GFGH  G+AL+ H D+D +AFTGST  
Sbjct: 188 ILKPSEKSPLTAIRIAQLALDAGIPKGVFNVLPGFGHTVGKALALHMDVDVLAFTGSTAI 247

Query: 249 GKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRL 308
            KQLL  AG SNMKRVWLEAGGKS N+VFAD PDL+ AA+A A+ I +NQG+VC AG+RL
Sbjct: 248 AKQLLIYAGQSNMKRVWLEAGGKSPNVVFADAPDLRAAATAAASAIAFNQGEVCTAGSRL 307

Query: 309 LLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLL 368
           L+E SI ++F+ LL +  Q W+PGH LDP TT+G ++D    D+V  +I  G+ +G  L+
Sbjct: 308 LVERSIREQFIPLLVEALQAWKPGHALDPETTVGAVVDQRQLDNVLRYISIGKEQGAQLI 367

Query: 369 DGRNAGLAAAIG----PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYG 424
            G N  L    G    P IF  V    +++REEIFGPVL +  F + E+AL +ANDS +G
Sbjct: 368 AGGNRALEDTGGLYVEPAIFDGVTNAMTIAREEIFGPVLSLITFDTAEEALAIANDSIFG 427

Query: 425 LGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFT 484
           L A VWT +LS+AH  +R L+AGSV+VN Y+ GDMT PFGG+KQSGNGRDKSLHA +K+T
Sbjct: 428 LAAGVWTSNLSKAHTFARGLRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYT 487

Query: 485 ELKTIWISL 493
           ELK  WI L
Sbjct: 488 ELKATWIKL 496


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: 616
Number of extensions: 15
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 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