GapMind for catabolism of small carbon sources

 

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

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate AO353_15035 AO353_15035 aldehyde dehydrogenase

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



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

 Score =  546 bits (1406), Expect = e-160
 Identities = 258/489 (52%), Positives = 358/489 (73%)

Query: 9   WEQRAQQLKIEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARA 68
           W+ +A  L+   +A I G+   A SG+TF  ++P  G  LA+VA+C  AD + AV +AR 
Sbjct: 7   WQGQAAALQFPTQALIEGKQRPAQSGQTFAAINPATGAVLAEVAACGNADVDAAVISARQ 66

Query: 69  TFNSGVWSQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAI 128
            F SGVWS  +P +RK  L+R A+L+  N EELALL++L+MGKP+ D+ +ID+PGAA   
Sbjct: 67  AFESGVWSARSPGERKQVLLRLAELIMANREELALLDSLNMGKPVMDAYTIDVPGAAGVF 126

Query: 129 HWTAEAIDKVYDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSV 188
            W AE++DK+YD++AP+  + L  +TRE +GVV A+VPWNFPL MA WKL PALA GNSV
Sbjct: 127 RWYAESLDKLYDQIAPSAQNVLATITREALGVVAAVVPWNFPLDMAAWKLAPALAAGNSV 186

Query: 189 VLKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKI 248
           +LKP+E+SP +A+R+ +LA+EAG+P GVLNVLPG G   GKAL LH+D+D LVFTGST++
Sbjct: 187 ILKPAEQSPFSALRLGELALEAGVPPGVLNVLPGLGEQAGKALGLHLDIDCLVFTGSTEV 246

Query: 249 AKQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRL 308
            K  M Y+ +SN+K++WLE GGKS N+VFAD  DL  AA+ AA  I FNQGEVC+A SRL
Sbjct: 247 GKYFMQYSAQSNLKQVWLECGGKSANLVFADCQDLDLAAQKAAFGIFFNQGEVCSANSRL 306

Query: 309 LVERSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLL 368
           LVERSI D+F+  ++  ++ W+PG+PLD  +T GA+VD++Q   ++ +I+   + GAK +
Sbjct: 307 LVERSIHDEFVERLMVQVERWQPGDPLDSSSTAGAIVDSRQTARIMKFIQQAERQGAKRV 366

Query: 369 AGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYG 428
            GG++++      +++PTIF GVT  M + ++E+FGPVL+V AFD    A+ +AND+ YG
Sbjct: 367 CGGQQSIINGSDNFIQPTIFTGVTADMPLFRDEVFGPVLAVTAFDDEASALQLANDSVYG 426

Query: 429 LAAGIWTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYT 488
           LAA +WT D+++AH+ AR +RAG+V VN  D  D+T PFGG KQSG GRD SLH+ +KYT
Sbjct: 427 LAASLWTDDLNRAHRVARQLRAGTVSVNSVDALDVTVPFGGGKQSGFGRDLSLHSFDKYT 486

Query: 489 ELKATWIKL 497
           +LK TW +L
Sbjct: 487 QLKTTWFQL 495


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: 645
Number of extensions: 23
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, 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