GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Caulo:CCNA_03695
          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:

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