Alignments for a candidate for acn in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Cupriavidus basilensis 4G11

Align Aconitate hydratase A; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate RR42_RS11270 RR42_RS11270 aconitate hydratase

Query= SwissProt::Q937N8
         (869 letters)



>FitnessBrowser__Cup4G11:RR42_RS11270
          Length = 865

 Score = 1496 bits (3872), Expect = 0.0
 Identities = 740/870 (85%), Positives = 800/870 (91%), Gaps = 6/870 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+ANRKPLPGT+LD+FD RAAV+AIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSL Q
Sbjct: 1   MNTANRKPLPGTQLDFFDTRAAVDAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLKQ 60

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
           ++ RK++LDFPWFPARVVCHDILGQTALVDLAGLRDAIA QGGDP  VNPVVP QL+VDH
Sbjct: 61  IIERKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAQGGDPVMVNPVVPTQLVVDH 120

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVECGGFDPDAFAKNRAIEDRRNEDRF FI+WTK+AFKNVDVIPPGNGI+HQINLE+M
Sbjct: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFDFINWTKKAFKNVDVIPPGNGILHQINLERM 180

Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
           SPV+   +GVA+PDT VGTDSHTP VDALGVIAIGVGGLEAE+VMLGRASWMRLPDI+GV
Sbjct: 181 SPVVQVKDGVAFPDTLVGTDSHTPMVDALGVIAIGVGGLEAESVMLGRASWMRLPDIIGV 240

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
           ELTGK QPGITATD VLALTEFLRKEKVV +YLEF GEG + LTLGDRATISNMAPE+G+
Sbjct: 241 ELTGKPQPGITATDTVLALTEFLRKEKVVSSYLEFFGEGTTHLTLGDRATISNMAPEFGS 300

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           TAAMF+IDEQTI YL+LTGR D  +KLVETYA+ AGLWADSLKNAEY RVL+FDLS+VVR
Sbjct: 301 TAAMFYIDEQTIKYLKLTGRDDALVKLVETYAKEAGLWADSLKNAEYPRVLRFDLSTVVR 360

Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
           N+AGPSNPHKR+PTS LA RGI+        +   GLMPDGAVIIAA+TSCTNT+NPRN+
Sbjct: 361 NIAGPSNPHKRVPTSELAARGIS-----GKVENEPGLMPDGAVIIAAVTSCTNTNNPRNM 415

Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
           +AA LLARNAN  GL RKPWVKSSLAPGSKAV LYLEEANLLP+LE+LGFG+VA+ACT+C
Sbjct: 416 VAAGLLARNANKLGLTRKPWVKSSLAPGSKAVTLYLEEANLLPELEQLGFGVVAYACTSC 475

Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
           NGMSGALDP IQ+E++DRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPVIQKEVVDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535

Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
           RFDIEKDVLGTD DGKPV LKDIWPSDEEIDA+VA SVKP QFRKVYEPMFA+TA +GE 
Sbjct: 536 RFDIEKDVLGTDADGKPVTLKDIWPSDEEIDAVVAASVKPAQFRKVYEPMFAVTADTGEK 595

Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
            SPLYDWR  STYIRRPPYWEGALAGER L  +RPLAVLGDNITTDHLSPSNAIML+SAA
Sbjct: 596 ASPLYDWREMSTYIRRPPYWEGALAGERALTGMRPLAVLGDNITTDHLSPSNAIMLDSAA 655

Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720
           GEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANPTL NEM VVDG+VK GSLARIEPEG
Sbjct: 656 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPTLKNEMVVVDGKVKPGSLARIEPEG 715

Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780
           KV RMWEAIETYM RKQPLI++AGADYGQGSSRDWAAKGVRLAGVE IVAEGFERIHRTN
Sbjct: 716 KVTRMWEAIETYMARKQPLIVVAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTN 775

Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840
           L+GMGVLPLEFKPGVNR TLG+DGTETYDVIG+R PR  LTLV++RKNGERVEVPVTCRL
Sbjct: 776 LVGMGVLPLEFKPGVNRATLGIDGTETYDVIGDRTPRCDLTLVMHRKNGERVEVPVTCRL 835

Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESSRATA 869
           D+ EEVSIYEAGGVL  FAQDFLESS+A A
Sbjct: 836 DTAEEVSIYEAGGVLQRFAQDFLESSKAAA 865


Lambda     K      H
   0.318    0.135    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: 2304
Number of extensions: 93
Number of successful extensions: 3
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: 869
Length of database: 865
Length adjustment: 42
Effective length of query: 827
Effective length of database: 823
Effective search space:   680621
Effective search space used:   680621
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: 56 (26.2 bits)

This GapMind analysis is from Sep 17 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