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_03695 CCNA_03695 aldehyde dehydrogenase

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



>lcl|FitnessBrowser__Caulo:CCNA_03695 CCNA_03695 aldehyde
           dehydrogenase
          Length = 506

 Score =  369 bits (946), Expect = e-106
 Identities = 203/476 (42%), Positives = 281/476 (59%), Gaps = 12/476 (2%)

Query: 23  FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82
           FI G++     G  F+  SP+ GR + ++A     D  RA++ A A      W++ + A 
Sbjct: 22  FIGGQWVAPADGRYFDNSSPIHGRKICEIARSQAIDIERALDAAHAA--KAGWARTSAAD 79

Query: 83  RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142
           R   L+R AD + +N+  LA  ET D GKPI ++ + DIP A     + A  +      +
Sbjct: 80  RSRILLRIADRMEENLAALATAETWDNGKPIRETLAADIPLAIDHFRYFAGCLRSQEGSI 139

Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202
           +   HD +     EP+GVVG I+PWNFPLLMACWKL PALA GN VVLKP+E++P + + 
Sbjct: 140 SEIDHDTIAYHFHEPLGVVGQIIPWNFPLLMACWKLAPALAAGNCVVLKPAEQTPASIMV 199

Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262
            A++ I   +PAGVLN++ G+G   GK LA    +  + FTG T   + +M YA + N+ 
Sbjct: 200 WAEM-IGDLLPAGVLNIVNGFGLEAGKPLASSPRIAKIAFTGETSTGRLIMQYAAQ-NLI 257

Query: 263 RIWLEAGGKSPNIVFADA----PDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKF 318
            + LE GGKSPNI F D      D    A    +  A NQGEVCT  SR LV+ SI +KF
Sbjct: 258 PVTLELGGKSPNIFFDDVAREDDDYLDKALEGFTMFALNQGEVCTCPSRALVQESIYEKF 317

Query: 319 LPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTL--- 375
           +   ++ +     G+PLDP T +GA    +Q+N +L Y++ G  +GAKLLAGG+R +   
Sbjct: 318 MERALKRVNAVVQGSPLDPATMIGAQASEEQLNKILGYMDIGRNEGAKLLAGGQRKILPG 377

Query: 376 EETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWT 435
           +   G YVEPT+F+G  N MRI QEEIFGPVL+V  F T EEA+ IANDT +GL AG+W+
Sbjct: 378 QLADGYYVEPTVFEG-HNKMRIFQEEIFGPVLAVTTFKTEEEALEIANDTAFGLGAGVWS 436

Query: 436 SDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491
            D ++ ++  R + AG VW N Y      A FGG+KQSG GR+     L+ Y + K
Sbjct: 437 RDANRCYRFGRGIEAGRVWTNCYHAYPAHAAFGGYKQSGVGRETHKMMLDHYQQTK 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: 641
Number of extensions: 24
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: 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 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