Alignments for a candidate for drdehyd-beta in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for drdehyd-beta in Caulobacter crescentus NA1000

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate CCNA_02352 CCNA_02352 membrane-bound aldehyde dehydrogenase, large subunit

Query= metacyc::MONOMER-20833
         (739 letters)



>FitnessBrowser__Caulo:CCNA_02352
          Length = 724

 Score =  356 bits (913), Expect = e-102
 Identities = 253/735 (34%), Positives = 360/735 (48%), Gaps = 59/735 (8%)

Query: 29  VIGFGLPLGAGRVQAATSAERG-----TQVPAFLEIRPDGTVRLLSPFMEGGQGTHTAMA 83
           V+  G  +G G + + T +  G     T+V A++ I  DG V + S   E GQG  TA+ 
Sbjct: 14  VLQSGAAVGGGLLLSFTMSSEGQAAGDTKVNAYVRIASDGKVTIASKVPEVGQGIKTALP 73

Query: 84  QIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMSVRMSYPTMRRLGALARAMLL 143
            ++ EELD D +   VE A           G ++ GGSM+  + Y  +RR+GA  RA+L+
Sbjct: 74  MLIAEELDVDWSAVTVEQAIADTKIY----GRQVAGGSMATTLEYDGLRRVGATVRALLI 129

Query: 144 QAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDMPVPDPASITLRDPSQFRW 203
            A A +W VP   L T+PG VV AA  R   YGELA +A  +  PDP S+TL+DP  FR 
Sbjct: 130 AAAAARWNVPADSLKTEPGFVVDAAGKRRASYGELAQAAAALTPPDPKSLTLKDPKAFRI 189

Query: 204 IGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGMTVGSLRNQSQVEGMKGVH 263
           IGK  K  +     TG+  Y ID+++  ML AA   AP  G  V S+ + +  + +KGV 
Sbjct: 190 IGKSHKSQNLDAIVTGQPTYGIDVRLPGMLFAAFAKAPVYGAKVASV-DLALAKAVKGVR 248

Query: 264 SVHVLPG---------AVAVVAERWWHAKRAVEAIQVDWQEAAADSALRVMPADFSSDKH 314
              ++ G          VAVVA+ WW A++  EA+Q+ W E    S   V    F++ K 
Sbjct: 249 DAFIIEGGTNLQGLLPGVAVVADSWWAARKGREALQIQWAEHPTASQSTV---GFAA-KA 304

Query: 315 REFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQLEPPSALARFNPDGTL 374
            E  AA   P R+  N+GDV  ALKGA   V A Y   ++ HA LEP +  A    DG +
Sbjct: 305 AELAAAP--PHRNLHNDGDVEAALKGAAKTVSAAYSYPFIAHAALEPQNCTAHVK-DGKV 361

Query: 375 EIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDSANPYPQAIALAKAV 434
           EIW P Q P+  RA +A+   +DP+ IT+H    GG FGR  + D      +A A+A  V
Sbjct: 362 EIWAPTQNPESGRALVARALNVDPSAITIHLIRGGGGFGRRLMNDY---MVEAAAIAAKV 418

Query: 435 SRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIEAVSATEGPTEALAGKQGDK 494
           + P++LIW+RE++   D  RP       A LD KG   A +    T G  E         
Sbjct: 419 NAPVQLIWTREDDMQHDFYRPGGWHNLTAGLDAKGGLTAWKNHFITFGEGETFN------ 472

Query: 495 IDPTAVEGLSGKSYAIPNKR-IAQIYVKGAPMLGYWRSVGNSLNDFFYESFLDELADKGG 553
               A+        A+ N R    +   G P  G+ R+ GN+   F  +SF DELA   G
Sbjct: 473 -TAAAMNATQFPCRAVANYRHDVSVMPLGFP-TGFLRAPGNNAFGFVIQSFTDELALAAG 530

Query: 554 HDPYELRLHLLRD--------------NPRLTTLLQAAGELSGGWKRGPFTAEDGTRRAR 599
            DP   R  LL +                R+  +L    E+SG  ++ P     GT    
Sbjct: 531 KDPVAFRRELLGEPRLLGEPGKGDSFHTGRMRGVLDLVAEMSGWGRKVP----KGT--GL 584

Query: 600 GVAMASPFGSHTAAIAEVSIENGKVKVHDIWQAIDPG-SIVNPAIVEAQVNGAVALGLSQ 658
           GVA       + A + +V++++G VKV  +W A D G  IVNP+  + Q+ G++   +  
Sbjct: 585 GVACHYSHLGYVAVVMQVTVKDGAVKVDKVWAAADVGRQIVNPSGADQQMQGSILDAIGS 644

Query: 659 TLLEEAVYVDGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPAVAPAVAN 718
           TL +   + +G     N+  +P+L  A    V VR   S     G+GEP  P    A+ N
Sbjct: 645 TLYQSITFENGAATNSNFGDFPLLRMADAPPVEVRYKLSDNNPTGLGEPAYPPAPAALCN 704

Query: 719 AVAQLTGQRVRSLPL 733
           A+   TG+R+RSLP+
Sbjct: 705 AIFAATGKRIRSLPI 719


Lambda     K      H
   0.317    0.134    0.394 

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: 1296
Number of extensions: 65
Number of successful extensions: 9
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: 739
Length of database: 724
Length adjustment: 40
Effective length of query: 699
Effective length of database: 684
Effective search space:   478116
Effective search space used:   478116
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 (21.7 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources