Alignments for a candidate for aldox-large in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for aldox-large in Cupriavidus basilensis 4G11

Align glycolaldehyde oxidoreductase large subunit (characterized)
to candidate RR42_RS26495 RR42_RS26495 carbon monoxide dehydrogenase

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



>FitnessBrowser__Cup4G11:RR42_RS26495
          Length = 802

 Score =  291 bits (746), Expect = 7e-83
 Identities = 229/790 (28%), Positives = 367/790 (46%), Gaps = 65/790 (8%)

Query: 4   VGKPVKRIYDDKFVTGRSTYVDDIRIPALY-AGFVRSTYPHAIIKRIDVSDALKVNGIVA 62
           VG  V R  D + + G+  +V DI +P L    F+RS   HA +  +     L+ + ++ 
Sbjct: 14  VGARVARKEDARHLHGKGRFVADIAMPGLQEVAFLRSPMAHARLLALHKPQGLE-HAVIG 72

Query: 63  VFTAKEINPLLKGGIRPWPTYIDIRSFRYSERKAFPENKVKYVGEPVAIVLGQDKYSVRD 122
                    ++     P        S++ S +      KV++VGEP+A+     +    D
Sbjct: 73  RDDMHGALDIVADSAFP--------SYQPSAQPPLAAGKVRFVGEPIAMAFAPTRAQAED 124

Query: 123 AIDKVVVEYEPLKPVIRMEEAEKDQ--VIIHEELKTNISYKIPFKAGEVDKAFSESDKVV 180
             +++V E + L  +  ++ A +      +HE  K N      F     DK F    K  
Sbjct: 125 IAERIVAELDELPALTDVDGARQASGTTRVHEHWKNN-----HFLTLTADKNFDTLSKTA 179

Query: 181 RVEAINE----RLIPNPMEPRGIVSRFEA--GTLSIWYSTQVPHYMRSEFARILGIPESK 234
            V    +    R    PME + +++ ++     L ++ +TQVPH +R+  +  LG+ + K
Sbjct: 180 SVVVSRKIDLARQCMVPMEGKAVLAYWDHQFDQLIVYSATQVPHMIRTVLSHCLGLEQEK 239

Query: 235 IKVSMPDVGGAFGAKVHLMPEELAVVASSIILGRPVRWTATRSEEMLA-SEARHNVFTGE 293
           ++V  PDVGGAFG K  L  EEL +   ++   +P R+   R E + A + +R + +   
Sbjct: 240 VRVISPDVGGAFGYKCVLQQEELCIAWLAMTYRKPFRFIEDRREHLTAGANSREHHYEVT 299

Query: 294 VAVKRDGTILGIKGKLLLDLGAYIT--VTAGIQPLIIPMMIPGPYKIRNLDIESVAVYTN 351
                 G +L +  ++ +D GAY     T G++P      +PGPY        +  V TN
Sbjct: 300 AYADARGRLLALDARIAIDGGAYSVWPFTIGLEPGQAIGNLPGPYAFDGYRCITECVATN 359

Query: 352 TPPITMYRGASRPEATYIIERIMSTVADELGLDDVSIREKNLVT--ELPYTNPFGLRYDS 409
            P    YRG +R    + +E +M  +A E+  +   IR +NLV    +PY N     +D 
Sbjct: 360 KPGFVPYRGVARTGVCFAMELLMDALAREVKREPWEIRCENLVQPESMPYVNVTNKHFDG 419

Query: 410 GDYVGLLREGVKRLGYYELKKWAEE---ERKKGHR-VGVGLAYYLEICSFGP-------- 457
           GDY   +R+  + +G   +++   +   +   G R +GVG   Y E  + G         
Sbjct: 420 GDYPASVRKAAQMIGLAGIRERQRQRLNDPSAGSRYLGVGFGTYTEQSAHGTSVFAAWGT 479

Query: 458 -----WEYAEVRVDERGDVLVVTGTTPHGQGTETAIAQIVADALQIDISRVRVIWGDTDT 512
                ++ A VR+   G + V  G   HGQG ET  AQI  + L ID+SRV+V+ GDT  
Sbjct: 480 PVIPGFDSATVRITPDGGLEVRVGVHSHGQGMETTFAQIANEILGIDVSRVKVVHGDTGV 539

Query: 513 VAASMGTYGSRSVTIGGSAAIKVAEKILDKMKRIAASTWNVDVQEVQYEKGEFKLKNDPS 572
              S GTY SRS+ + G A  +  + ++ ++ +I A        E     G  K   D +
Sbjct: 540 TPFSTGTYASRSLVMSGGAVSRACKALVPRLLKIGAHMLQRPEGEATLAGGSVK-AGDAA 598

Query: 573 KKMSWDDVASIAY-------RSHDP-GLVEKIIYENDV---TFPYGVHIATVEVD-DTGV 620
             +S  ++A+  Y        + DP GL   + Y+  V   +F Y  H A VEVD D+G 
Sbjct: 599 VPIS--EIANAWYINPQRLPANVDPTGLETTMGYKPSVDTGSFTYSTHAALVEVDTDSGH 656

Query: 621 ARVLEYRAYDDIGKVVNPALAEAQIHGGGVQAVGQALYEQALLNENGQ-LIVTYADYYVP 679
             +L+Y   +D G +VNP + E Q +GG  Q +G A++E+   + NGQ L  T ADY +P
Sbjct: 657 VEILDYVVVEDCGTMVNPMVVEGQTYGGVAQGIGTAMFEEMRYDGNGQPLASTLADYMLP 716

Query: 680 TAVEAPKFTSVFADQYHPSNYPTGSKGVGEAALIVGPAVIIRALEDAIGT---RFTKTPT 736
              E P       +   P +   G+KG+GE   I  PA I  A+ DA+G+      +TP 
Sbjct: 717 GPTEIPSIRIHHFETPSP-HTEFGAKGMGEGGAIAPPAAIFNAVNDALGSFGVELLETPL 775

Query: 737 TPEEILRAIA 746
           TP ++L A+A
Sbjct: 776 TPRKVLEALA 785


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: 1346
Number of extensions: 80
Number of successful extensions: 10
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: 802
Length adjustment: 41
Effective length of query: 708
Effective length of database: 761
Effective search space:   538788
Effective search space used:   538788
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