Alignments for a candidate for mmsA in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Cereibacter sphaeroides ATCC 17029

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_011842384.1 RSPH17029_RS17490 aldehyde dehydrogenase family protein

Query= BRENDA::Q97YT9
         (492 letters)



>NCBI__GCF_000015985.1:WP_011842384.1
          Length = 791

 Score =  233 bits (593), Expect = 2e-65
 Identities = 148/453 (32%), Positives = 232/453 (51%), Gaps = 17/453 (3%)

Query: 18  YINGEFIDSKTDTIGKAYNPAKDEIIAEVPFSAKDEVEEAIQSAQEAFEKWREVPITTRI 77
           YI+G F  ++T  I +  NPA  EI+A +P + + E+E A+ +A+ AF  W ++P   R 
Sbjct: 36  YIDGAFTGAETAAI-EVENPATGEILARIPAAGEAEIEAAVAAARAAFSGWSQLPGFERA 94

Query: 78  QYLFALKNRLEEYSETIARIIVQNHGKTIQEARGDMRRTIENVEAAISAAYTLYKGEHLD 137
           +YL+A+   L++     + +   ++GK I+E R        +V  AI   Y      H  
Sbjct: 95  RYLYAIARGLQKRERFFSVLETLDNGKAIRETR------TADVPLAIRHFY-----HHAG 143

Query: 138 QVSQEVDETVVREPLGVFGIITPFNFPTMVPFWFLPYAIVLGNTVVVKPSEITPVPMDFI 197
             +   +E    EPLGV G + P+NFP ++  W +  A+  GNTVV+KP+++TP+     
Sbjct: 144 WAAVLGEEFPGHEPLGVCGQVIPWNFPMLMLAWKIAPALAAGNTVVLKPADLTPLTAVAF 203

Query: 198 IRIFDEIKLPRGVVNVVHGAKDVVDEFLTNKLVQGVTFVGSTRVGKYIYENAGKNGKKAI 257
             + DEI LPRGVVN+VHG  +     + +  V  V F GST VG+ I      +GK   
Sbjct: 204 AEMLDEIGLPRGVVNIVHGGAETGALLVRHPGVAKVAFTGSTAVGREIRRATAGSGKSLT 263

Query: 258 VQAGAKNFVVVMPDADLNKAIPSIVSAFFGNAGQRCLAAANLVAVGNIYDEVKRKFIEAS 317
           ++ G K+  VV  DADL+ A+  +V   + N G+ C A + L+    I +    K     
Sbjct: 264 LELGGKSPFVVCADADLDAAVEGVVEGVWFNQGEVCCAGSRLLLQEGIAERFLAKLRARM 323

Query: 318 KQLKIGYGLDESVDMGPVVTKDAKKRIIGYIEKGIEEGAKLLLDGRDVKVPEYPNGYFLG 377
           +++++G  LD+S DMG +V+   K RI   I     EG +L         P    G+F+ 
Sbjct: 324 EKIRVGDPLDKSTDMGAIVSARQKARIEELIAGAAREGYRL----EQAACPLPAAGHFVA 379

Query: 378 PTVFDEVTPEMVIAKEEIFGPVASIIHVKNLDEAINIINRSNYGNASSIFTTSGYYARKF 437
           P  F +  P   +A+ EIFGP+A     + +DEA+ + N + YG A+S+++ +   A + 
Sbjct: 380 PGFFADTEPAATVAQVEIFGPIAVTTTFRTVDEAVALANNTPYGLAASVWSENINAATEL 439

Query: 438 RREVNTGNIGINIGVAAPMAFFPFGGRKESFFG 470
              +  G + IN       A   FGG KES FG
Sbjct: 440 AARIRAGVVWINASNLFD-AGASFGGMKESGFG 471



 Score = 66.6 bits (161), Expect = 3e-15
 Identities = 62/225 (27%), Positives = 100/225 (44%), Gaps = 8/225 (3%)

Query: 39  KDEIIAEVPFSAKDEVEEAIQSAQEAFEKWREVPITTRIQYLFALKNRLEEYSETIARII 98
           K E +   P S + ++  A+++A +A  K        R Q LF L   +   +E +A  +
Sbjct: 541 KGEALGLAPVSGRKDIRNAVEAALKA--KGWAANAHGRAQVLFFLAENIAARAEDLAAAL 598

Query: 99  VQNHGKTIQEARGDMRRTIENVEAAISAAYTLYKGEHLDQVSQEVDETV-VREPLGVFGI 157
           VQ  G    EA  ++R  IE V      A    K +     ++    T+ V+EPLGV G+
Sbjct: 599 VQG-GAGRSEAAAEVRSLIERVFFYAGMAD---KDDGRIHATKPRHLTLSVKEPLGVVGV 654

Query: 158 ITPFNFPTMVPFWFLPYAIVLGNTVVVKPSEITPVPMDFIIRIFDEIKLPRGVVNVVHGA 217
           + P   P +     +   I  GN VV  PS    +    + +IFD   LP GVVN+V G 
Sbjct: 655 LAPDEAPLLSLMSLILPLIAAGNRVVAVPSPAQALLAQPLTQIFDTSDLPGGVVNLVTGD 714

Query: 218 KDVVDEFLT-NKLVQGVTFVGSTRVGKYIYENAGKNGKKAIVQAG 261
           ++++   L  +  V G+ + GS +    +   +  N K+     G
Sbjct: 715 RNLLARTLAEHDAVDGIWYHGSAKGAAEVEALSAGNLKQVWTNGG 759


Lambda     K      H
   0.319    0.139    0.398 

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: 841
Number of extensions: 36
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 492
Length of database: 791
Length adjustment: 37
Effective length of query: 455
Effective length of database: 754
Effective search space:   343070
Effective search space used:   343070
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 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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