GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuC in Caulobacter crescentus NA1000

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate CCNA_00424 CCNA_00424 aldehyde dehydrogenase

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



>lcl|FitnessBrowser__Caulo:CCNA_00424 CCNA_00424 aldehyde
           dehydrogenase
          Length = 479

 Score =  274 bits (700), Expect = 6e-78
 Identities = 174/473 (36%), Positives = 259/473 (54%), Gaps = 15/473 (3%)

Query: 23  FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82
           +I+G + D  +  T + ++P        ++    AD ++AV  AR  F S  +SQ +  +
Sbjct: 8   YIDGAWVDPAAPNTLDVINPATEEVCGVISMGSEADVDKAVRAARKAFAS--FSQTSREE 65

Query: 83  RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVY--D 140
           R   L R     +K  E++A   T +MG P   +           +  TA A+ K Y  +
Sbjct: 66  RIDILERIIAEYQKRFEDMAKAITEEMGAPAWLAQRAQAAMGIGHVQ-TAAAVLKGYKFE 124

Query: 141 EVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTA 200
           E   T       + +EP+GV   I PWN+P+     K+GPA+ATG ++VLKPSE +P + 
Sbjct: 125 EDRGTTR-----IVKEPIGVCAFITPWNWPVNQIACKVGPAIATGCTMVLKPSEIAPFSG 179

Query: 201 IRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESN 260
               ++   AG+PAGV N++ G G TVG AL+ H +VD + FTGST+   ++   A  + 
Sbjct: 180 YIWTEIMHAAGVPAGVFNLVNGDGPTVGAALSRHPEVDMVSFTGSTRAGIEVAKNAAPT- 238

Query: 261 MKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLP 320
           +KR+  E GGKSPNI+  DA D   A     +++  N G+ C A +R+LV  +  D+ + 
Sbjct: 239 VKRVHQELGGKSPNIILDDA-DFSRAVAGGVASVMMNSGQSCNAPTRMLVPGARMDEVIA 297

Query: 321 MVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETG- 379
           +   A +    G+P +    +G +V   Q N +   I+ G  +GA L+ GG    E    
Sbjct: 298 IAKAAAESHTVGDP-NGNHKMGPVVSETQWNKIQGLIQKGIDEGATLVTGGVGRPEGLDK 356

Query: 380 GTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDIS 439
           G YV+PT+F  VTN M IA+EEIFGPV+S++ +DT +EAV + NDT YGLAA +   D  
Sbjct: 357 GYYVKPTVFANVTNEMTIAKEEIFGPVVSILGYDTVDEAVTVGNDTEYGLAAYVSGGDQD 416

Query: 440 KAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKA 492
           +  K A  +RAG V +N   G D+ APFGG+K SGNGR+   HA  ++ E KA
Sbjct: 417 EVRKVASRLRAGQVTLNG-AGPDLMAPFGGYKMSGNGREWGDHAFGEFLETKA 468


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: 587
Number of extensions: 26
Number of successful extensions: 6
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: 479
Length adjustment: 34
Effective length of query: 463
Effective length of database: 445
Effective search space:   206035
Effective search space used:   206035
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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