GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuC in Herbaspirillum seropedicae SmR1

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate HSERO_RS09465 HSERO_RS09465 aldehyde dehydrogenase

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



>lcl|FitnessBrowser__HerbieS:HSERO_RS09465 HSERO_RS09465 aldehyde
           dehydrogenase
          Length = 506

 Score =  376 bits (966), Expect = e-109
 Identities = 214/479 (44%), Positives = 287/479 (59%), Gaps = 18/479 (3%)

Query: 23  FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82
           FI G++   V GE FE +SPV GR   +VA     D   A++ A A   S  W + +P +
Sbjct: 22  FIGGKFVPPVKGEYFENISPVIGRAFCEVARSSAEDVELALDAAHAAKKS--WGKTSPTE 79

Query: 83  RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142
           R   L++ AD +  N+E LA  ETLD GKPI ++ + DIP A     + A A+      +
Sbjct: 80  RANMLLKIADRMEANLELLATAETLDNGKPIRETMAADIPLAIDHFRYFAAAVRTQEGSI 139

Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202
            P  +D       EP+GVVG I+PWNFP+LMA WKL PALA GN VVLKP+E++P + + 
Sbjct: 140 CPIDNDTYAYHFHEPLGVVGQIIPWNFPILMAVWKLAPALAAGNCVVLKPAEQTPASIMV 199

Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262
           + +L  +  IP GV+N++ G+G   GK LA +  +  + FTG T   + +M YA + N+ 
Sbjct: 200 LIELIADL-IPPGVVNIVQGFGVEAGKPLASNKRIAKIAFTGETTTGRLIMQYASQ-NLI 257

Query: 263 RIWLEAGGKSPNIVFADAPD-----LQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDK 317
            + LE GGKSPNI FAD  D        A E  A   A NQGEVCT  SR+LV+ SI ++
Sbjct: 258 PVTLELGGKSPNIFFADVLDKDDDFFDKALEGFA-MFALNQGEVCTCPSRVLVQESIYER 316

Query: 318 FLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEE 377
           F+   ++ +   K GNPLD  T +GA    +Q+  +LSYI+ G ++GAK+LAGG R  EE
Sbjct: 317 FIERALKRVAAIKQGNPLDKSTMIGAQASQEQLEKILSYIDIGKQEGAKVLAGGGR--EE 374

Query: 378 TGGT-----YVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAG 432
            GG      YV+PT+F G  N MRI QEEIFGPV+SV  F   EEA+AIANDT YGL AG
Sbjct: 375 LGGDLASGYYVKPTVFQG-NNKMRIFQEEIFGPVVSVTTFKDEEEALAIANDTLYGLGAG 433

Query: 433 IWTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491
           +WT D ++A +  R ++AG VW N Y      A FGG+KQSG GR+     L+ Y + K
Sbjct: 434 LWTRDGTRAFRMGREIQAGRVWTNCYHLYPAHAAFGGYKQSGIGRENHKMMLDHYQQTK 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: 607
Number of extensions: 27
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 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