GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuC in Pseudomonas fluorescens FW300-N1B4

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate Pf1N1B4_4355 Gamma-glutamyl-aminobutyraldehyde dehydrogenase (EC 1.2.1.-)

Query= metacyc::MONOMER-11560
         (497 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4355
           Gamma-glutamyl-aminobutyraldehyde dehydrogenase (EC
           1.2.1.-)
          Length = 496

 Score =  784 bits (2025), Expect = 0.0
 Identities = 380/495 (76%), Positives = 435/495 (87%)

Query: 3   TLTRADWEQRAQQLKIEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRA 62
           T TR+DWEQR Q L +EGRAFI+G+Y  A+SG+TFEC+SPVDGRFLA +AS D ADAN A
Sbjct: 2   TNTRSDWEQRFQSLTLEGRAFIDGQYCPALSGDTFECISPVDGRFLANIASTDEADANAA 61

Query: 63  VENARATFNSGVWSQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIP 122
           V+ AR TF SG+W++L PA+RK  LIRFADL+ +N EELALLETLDMGKPI DS SIDIP
Sbjct: 62  VQVARRTFESGIWAKLPPAERKRVLIRFADLILQNQEELALLETLDMGKPISDSMSIDIP 121

Query: 123 GAAQAIHWTAEAIDKVYDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPAL 182
             A AI W+AEAIDK+YDEVA TPHDQLGL+TREP GVV AIVPWNFPL+MA WK  PAL
Sbjct: 122 ATANAIRWSAEAIDKIYDEVAATPHDQLGLITREPAGVVAAIVPWNFPLIMASWKFAPAL 181

Query: 183 ATGNSVVLKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVF 242
           A GNS +LKPSEKSPLTAIRIAQLA+EAGIP GV NVLPG+GHTVGKALALHMDVD L F
Sbjct: 182 AAGNSFILKPSEKSPLTAIRIAQLALEAGIPKGVFNVLPGFGHTVGKALALHMDVDVLAF 241

Query: 243 TGSTKIAKQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVC 302
           TGST IAKQL++YAG+SNMKR+WLEAGGKSPN+VFADAPDL+AAA AA SAIAFNQGEVC
Sbjct: 242 TGSTAIAKQLLIYAGQSNMKRVWLEAGGKSPNVVFADAPDLRAAARAAVSAIAFNQGEVC 301

Query: 303 TAGSRLLVERSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHK 362
           TAGSRLLVERSI+++F+P++VEAL+ WKPG+ LDP+TTVGA+VD +Q++ VL YI+ G  
Sbjct: 302 TAGSRLLVERSIREQFIPLLVEALQAWKPGHALDPETTVGAVVDQRQLDNVLRYIQVGKD 361

Query: 363 DGAKLLAGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIA 422
            GA+L+AGG RTL +TGG YVEP IFDGVTNAM IA+EEIFGPVLS+I FDTAEEA+ IA
Sbjct: 362 QGAQLIAGGNRTLADTGGLYVEPAIFDGVTNAMTIAREEIFGPVLSLITFDTAEEALQIA 421

Query: 423 NDTPYGLAAGIWTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLH 482
           ND+ +GLAAG+WTS++SKAH  AR +RAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLH
Sbjct: 422 NDSIFGLAAGVWTSNLSKAHTFARGLRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLH 481

Query: 483 ALEKYTELKATWIKL 497
           A +KYTELKATWIKL
Sbjct: 482 AFDKYTELKATWIKL 496


Lambda     K      H
   0.316    0.132    0.390 

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: 762
Number of extensions: 20
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: 497
Length of database: 496
Length adjustment: 34
Effective length of query: 463
Effective length of database: 462
Effective search space:   213906
Effective search space used:   213906
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 (21.6 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, 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