Alignments for a candidate for aldox-large in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for aldox-large in Sinorhizobium meliloti 1021

Align glycolaldehyde oxidoreductase large subunit (characterized)
to candidate SM_b20132 SM_b20132 dehydrogenase

Query= metacyc::MONOMER-18071
         (749 letters)



>FitnessBrowser__Smeli:SM_b20132
          Length = 772

 Score =  308 bits (789), Expect = 7e-88
 Identities = 231/763 (30%), Positives = 374/763 (49%), Gaps = 33/763 (4%)

Query: 4   VGKPVKRIYDDKFVTGRSTYVDDIRIPA-LYAGFVRSTYPHAIIKRIDVSDALKVNGIVA 62
           VGK VKR    + VTG + Y  D+ +P  L+A   RS   HA I+ ID S AL + G+ A
Sbjct: 19  VGKSVKRSDTLEKVTGTARYAGDVALPGMLHAKMKRSNIAHARIRSIDTSKALALKGVKA 78

Query: 63  VFTAKEINPLLKGGIRPWPTYIDIRSFRYSERKAFPENKVKYVGEPVAIVLGQDKYSVRD 122
           V T +++  +L  G  P P     RS   ++ +   +++V+Y GE VA V    +     
Sbjct: 79  VLTHEDVPRVLHAG-SPHP-----RSASVTKDQYILDDRVRYWGEGVAAVAAVSEEIAER 132

Query: 123 AIDKVVVEYEPLKPVIRMEEAEKDQVI-IHEEL--KTNISYKIPFKAGEVDKAFSESDKV 179
           A+  + VEYEPL  +  +E A       IHE    +  +   +    G+VD+ F+E+D +
Sbjct: 133 AVALIEVEYEPLPGLFTIEAASVPGAPPIHENGLDRNQVLPPVFVTRGDVDRGFAEADLI 192

Query: 180 VRVEAINERLIPNPMEPRGIVSRFEA-GTLSIWYSTQVPHYMRSEFARILGIPESKIKVS 238
           +  E    R  P  MEP   VS+++  G L++W STQ    +R   A +LG+P +K++V 
Sbjct: 193 LEREYDLGRPTPAYMEPNVCVSQWDGNGKLTMWTSTQSAFMVRGTLAEVLGVPLNKVRVI 252

Query: 239 MPDVGGAFGAKVHLMPEELAVVASSIILGRPVRWTATRSEEMLASEARHNVFTGEVAVK- 297
           +  +GG FGAK  L   E      +   GRPV+   +R E  L   +RH    G++ +K 
Sbjct: 253 VDHMGGGFGAKQDLFQNEFLCALLARQTGRPVKMEFSRKETFLGGRSRH---PGKIWLKQ 309

Query: 298 ---RDGTILGIKGKLLLDLGAYITVTAGIQPLIIPMMIPGPYKIRNLDIESVAVYTNTPP 354
              +DG I+  + ++  + GAY +   G+   +    +   Y+  N+ +E   +YTN+P 
Sbjct: 310 GFTKDGRIVAREARVTFNSGAYGSHGPGVTN-VGTAALTSLYRCENVRLEGRCIYTNSPI 368

Query: 355 ITMYRGASRPEATYIIERIMSTVADELGLDDVSIREKNLVTE---LPYTNPFGLRYDSGD 411
              +RG    +  Y ++ +M   A++LG D    +  N V E    P  +P  + +  GD
Sbjct: 369 AGAFRGYGVVQTYYALDLMMDEAAEKLGFDPAEFKLMNAVREGDIAPSGHPI-VGHGLGD 427

Query: 412 YVGLLREGVKRLGYYELKKWAEEERKKGHRVGVGLAYYLEICSFGPWEY--AEVRVDERG 469
            +   R  ++   ++EL++  + E  K   +G+G   +      G  E   A V+++E G
Sbjct: 428 CI---RRVMEETNWHELRRREKPETVKRRGIGIGCEMHGSSAYPGIKEQGNAIVKMNEDG 484

Query: 470 DVLVVTGTTPHGQGTETAIAQIVADALQIDISRVRVIWGDTDTVAASMGTYGSRSVTIGG 529
            V ++TGT   G G  TA++QIVA+ L +    V V+ GDTD V   +G + S +  +GG
Sbjct: 485 TVTLITGTAGLGTGAHTALSQIVAEELGVPFEAVSVVQGDTDIVPWDIGAFASHTTYLGG 544

Query: 530 SAAIKVAEKILDKMKRIAASTWNVDVQEVQYEKGEFKLKNDPSKKMSWDDVASIAYRSHD 589
            AA   A  +  ++   AA     + + +    G   + N  ++ +   +          
Sbjct: 545 RAAQLAAADVRRQVLEHAAPMLKAEPENLAIRDGFVVVTNGSNRSIRLSEAVGPQRGMPA 604

Query: 590 PGLVEKIIYENDVTFPYGVHIATVEVD-DTGVARVLEYRAYDDIGKVVNPALAEAQIHGG 648
             LV    Y    ++ +  H A VEVD +TG   VL+     +IG+V++P  A  QI GG
Sbjct: 605 VQLVGVGTYMPTKSYSFAAHFAEVEVDTETGEVAVLQVVPVHEIGRVIHPIAAAGQIEGG 664

Query: 649 GVQAVGQALYEQAL--LNENGQLIVTYADYYVPTAVEAPKFTSVFADQYHPSNYPTGSKG 706
             Q +G  L E  +  L +   L  ++ DY +P +++ P   ++  +       P G+KG
Sbjct: 665 IQQGIGHTLSEDYVIDLTDGRSLNPSFVDYKMPLSMDMPSIRTIILETAPDPGGPYGAKG 724

Query: 707 VGEAALI-VGPAVIIRALEDAIGTRFTKTPTTPEEILRAIASK 748
           VGE  +I +GPA I  A+ DAIG RF   P TPE++L A+ SK
Sbjct: 725 VGEDPIIAIGPA-IANAIYDAIGVRFHHYPITPEQVLNALKSK 766


Lambda     K      H
   0.317    0.136    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: 1322
Number of extensions: 74
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: 749
Length of database: 772
Length adjustment: 40
Effective length of query: 709
Effective length of database: 732
Effective search space:   518988
Effective search space used:   518988
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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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