GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Pseudomonas stutzeri RCH2

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate GFF657 Psest_0671 NAD-dependent aldehyde dehydrogenases

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



>FitnessBrowser__psRCH2:GFF657
          Length = 506

 Score =  353 bits (905), Expect = e-101
 Identities = 205/483 (42%), Positives = 282/483 (58%), Gaps = 12/483 (2%)

Query: 16  LKIEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVW 75
           LK     FINGE+ + V+G+ F  LSPV+G+ +A+    D AD  +A++ A A  ++  W
Sbjct: 15  LKARYGNFINGEFVEPVNGQYFTNLSPVNGQPIAEFPRSDAADIEKALDAAHAAADA--W 72

Query: 76  SQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAI 135
            + +   R   L++ AD + +N+E LA+ ET D GK + ++ + DIP AA    + A  I
Sbjct: 73  GKTSVQARSLILLQIADRIEQNLEMLAVTETWDNGKAVRETLNADIPLAADHFRYFAGCI 132

Query: 136 DKVYDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEK 195
                  A            EP+GVVG I+PWNFP+LMA WKL PALA GN VVLKP+E+
Sbjct: 133 RAQEGTSAEIDEHTAAYHFHEPLGVVGQIIPWNFPILMAAWKLAPALAAGNCVVLKPAEQ 192

Query: 196 SPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVY 255
           +PL  I +    I   +P GVLNV+ GYG   G+ALA    +  + FTGST +   +M  
Sbjct: 193 TPL-GITVLMEVIGDLLPPGVLNVVQGYGREAGEALASSKRIAKIAFTGSTPVGSHIMKR 251

Query: 256 AGESNMKRIWLEAGGKSPNIVFADAPDLQAA-AEAAASAIA---FNQGEVCTAGSRLLVE 311
           A E+ +    +E GGKSPNI F D    +    E AA  +    FNQGEVCT  SR LV+
Sbjct: 252 AAEAIIPST-VELGGKSPNIYFEDIMQAEPTFIEKAAEGLVLGFFNQGEVCTCPSRALVQ 310

Query: 312 RSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGG 371
            SI   F+  V++ +   K G+PLD +T VGA    QQ + ++SY+E    +GA++L GG
Sbjct: 311 ESIYAPFMEAVMKKVAQIKRGDPLDTETMVGAQASQQQFDKIMSYLEIAKGEGAEVLTGG 370

Query: 372 KRTLEETG---GTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYG 428
                E     G Y++PT+  G TN MR+ QEEIFGPV+ V  F    EA+AIANDT YG
Sbjct: 371 AAEKLEGSLATGYYIQPTLLKG-TNQMRVFQEEIFGPVIGVTTFKDEAEALAIANDTEYG 429

Query: 429 LAAGIWTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYT 488
           L AG+WT DI++A++  RA++AG VW N Y      A FGG+K+SG GR+     L+ Y 
Sbjct: 430 LGAGVWTRDINRAYRMGRAIKAGRVWTNCYHLYPAHAAFGGYKRSGVGRETHKMILDSYQ 489

Query: 489 ELK 491
           + K
Sbjct: 490 QTK 492


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: 628
Number of extensions: 41
Number of successful extensions: 7
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: 506
Length adjustment: 34
Effective length of query: 463
Effective length of database: 472
Effective search space:   218536
Effective search space used:   218536
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 (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