Alignments for a candidate for DVU3033 in Malonomonas rubra DSM 5091

GapMind for catabolism of small carbon sources

Alignments for a candidate for DVU3033 in Malonomonas rubra DSM 5091

Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate WP_072906845.1 BUB13_RS06175 4Fe-4S dicluster domain-containing protein

Query= uniprot:Q726S3
         (717 letters)



>NCBI__GCF_900142125.1:WP_072906845.1
          Length = 719

 Score =  662 bits (1709), Expect = 0.0
 Identities = 334/719 (46%), Positives = 464/719 (64%), Gaps = 5/719 (0%)

Query: 1   MQNSKTLKEYRKELQESLDNEFLRNAMDKFAVAYRASRANAFKDIDEKAIIAEVADAKDH 60
           M N +  K+YR+ + ++L    L++A+ KF  A+  +R NAF   D +A+  E++  K  
Sbjct: 1   MMNKQRSKDYRQRIDKALATPKLQDALHKFGDAFLVARGNAFAKYDFEAMRDEISQMKTS 60

Query: 61  AAKNMDTLYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETH 120
             +N   L  QF   AE  G  V+LA+TA +AN  IA +A+    K A+KSKSM +EETH
Sbjct: 61  VRENHAELLQQFTQNAEAAGATVYLAKTAEDANNYIAELAKKKGAKLAVKSKSMASEETH 120

Query: 121 LNHRLEEDNVEVIETDLGEWIIQMRHEGPSHMVMPAIHLSRYQVADLFSEVTKQKQEVDI 180
           LN  LE+   + +ETDLGEWIIQ+  + PSHMVMPAIH+ + +VA+LFS+ T + ++ +I
Sbjct: 121 LNIALEKAGTKALETDLGEWIIQLAGQRPSHMVMPAIHMFKEEVAELFSKETGKTEQAEI 180

Query: 181 QRLVKVARRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGL 240
             LV+VAR +LR  +  A++GI+GAN AVAETG I LVTNEGNARL +TLP+ HVAL G+
Sbjct: 181 AHLVEVARNQLRQGYLDAEIGITGANIAVAETGGIALVTNEGNARLASTLPKTHVALVGI 240

Query: 241 DKLVPTLHDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRKEMHIVFLDNGRRA 300
           +KLVPTL DA + ++VLP+NATGQ +TSYVTWI GA  C+      K++HIV LDNGR  
Sbjct: 241 EKLVPTLEDATKVVRVLPKNATGQPLTSYVTWIRGAVPCDG---EEKDLHIVLLDNGRST 297

Query: 301 LAEDPLFSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLV 360
           LAE P     L C+RCGACANVCPVY+ VGGH  GHIYIGAIG+ILT FFHG + A  +V
Sbjct: 298 LAESPQCQDALNCIRCGACANVCPVYQTVGGHVFGHIYIGAIGIILTAFFHGLENAAEIV 357

Query: 361 QNCINCESCKHICAGGIDLPRLIKEIRARLNEEEGMPV-ETTLMGKMLKNRKLFHTLLRF 419
           + CI C SC  IC   IDL  +I  +R  + EEEG+   +  +  K+++NRKLFH L+R 
Sbjct: 358 RACIGCRSCVAICPSKIDLEEIILSLRETIGEEEGIGAGKDIVFRKVMRNRKLFHGLIRA 417

Query: 420 AKWAQKPVTGGTPYIRHLPQIFAKDHGFKALPAIADKPFRDEWETVRPRIAKPKLRIALF 479
           A   QKPVT G   IRHLP  F+    ++ LPA+A+KP RD        + KP+ R+ALF
Sbjct: 418 ASVMQKPVTRGESSIRHLPLFFSSLTEWRTLPAVAEKPLRDVILQQEQEVKKPRYRVALF 477

Query: 480 SGCVQDFVYPEQMKAAVKVIASQNVDIDFPMDQSCCGLPVQMMGEREATIEVARQNVMAF 539
            GC  DF+YPE     V V+ + +V++ +P +Q+CCG+P    G++E  IE+A+QN+ A 
Sbjct: 478 GGCANDFLYPELGLDLVTVMNALDVEVFYPQEQNCCGVPALYSGDKETAIELAKQNIDAM 537

Query: 540 DAARYDYIVTLCASCASHLKETYPKLLTGHPEMTTRVRQFSNKIIDFSSFVHDVLGMKSD 599
                D+++T C +C   L+  + + L  +P    +  + +   +D + FV + LG    
Sbjct: 538 LEGNPDFVLTTCPTCTMALQRDFVEHLKDNPAWAAKAERLAEITVDAAGFVVNQLGAADQ 597

Query: 600 AFKGGSNEKVAYHSSCHLCRGLGVVEQPRNLIAASGATYCKAEEEDVCCGFGGTFS-AKF 658
             +  ++EKV YH SCHL RG GV ++PR LI  +G    + +  D CCGFGG++S    
Sbjct: 598 FKQLAASEKVTYHDSCHLKRGAGVWKEPRQLIETAGHDLVEMDHADRCCGFGGSYSLTSH 657

Query: 659 PELSAELLRKKLDNVEATGAGRLVADCPGCIMQLRGGMEKRGGKVKVGHVAELLAENLK 717
           PE+S  +L  KL ++  +GA  +  DCPGC+MQ+RGG+EK+  KV+  H  ELLAE L+
Sbjct: 658 PEISKRILGDKLQDIAESGASCVAMDCPGCMMQIRGGLEKQDSKVRAQHTIELLAEALR 716


Lambda     K      H
   0.321    0.135    0.402 

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: 1305
Number of extensions: 53
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: 717
Length of database: 719
Length adjustment: 40
Effective length of query: 677
Effective length of database: 679
Effective search space:   459683
Effective search space used:   459683
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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