Alignments for a candidate for acn in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Acidovorax sp. GW101-3H11

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 Ac3H11_2323 2-methylcitrate dehydratase FeS dependent (EC 4.2.1.79)

Query= SwissProt::Q937N8
         (869 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2323
          Length = 889

 Score = 1391 bits (3601), Expect = 0.0
 Identities = 705/875 (80%), Positives = 771/875 (88%), Gaps = 9/875 (1%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+  R+PLPGT LDYFDARAAVE +QPGA+  LPYT+RV AE++VRR DPAT+ D L Q
Sbjct: 2   MNTLFRRPLPGTDLDYFDARAAVETLQPGAWATLPYTARVHAESIVRRADPATVNDCLRQ 61

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
           L+ RKRD DFPW+PARVVCHDILGQTALVDLAGLRDAIA  GGDPA+VNPVVPVQLIVDH
Sbjct: 62  LIERKRDRDFPWYPARVVCHDILGQTALVDLAGLRDAIAKGGGDPAQVNPVVPVQLIVDH 121

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFI+WTK+AF NVDVIP GNGIMHQINLEKM
Sbjct: 122 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIEWTKKAFANVDVIPAGNGIMHQINLEKM 181

Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
           SPV+HAD GVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRAS MRLP++VGV
Sbjct: 182 SPVVHADRGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASMMRLPEMVGV 241

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
           ELTG+RQ GITATD+VLALTEFLRK KVVGAYLEF GEGA+ LTLGDRATISNMAPEYGA
Sbjct: 242 ELTGQRQDGITATDVVLALTEFLRKAKVVGAYLEFFGEGAAKLTLGDRATISNMAPEYGA 301

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           TAA+F IDEQT+DYLRLTGR   Q+KLVETYA+TAGLWAD+L  A Y+R L+FDLS+VVR
Sbjct: 302 TAALFCIDEQTLDYLRLTGREARQVKLVETYAKTAGLWADALAGAVYDRTLRFDLSTVVR 361

Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
           N+AGPSNPH R+ TS LA RGIA     A     EG MPDGAV+IAAITSCTNTSNPRNV
Sbjct: 362 NLAGPSNPHARVATSDLAARGIAGPW--ALPSPGEGTMPDGAVVIAAITSCTNTSNPRNV 419

Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
           IAAALLARNA+  GL RKPWVK+SLAPGS+ VELYL+EA LL DLE LGFGIVAFACTTC
Sbjct: 420 IAAALLARNAHRLGLTRKPWVKTSLAPGSRVVELYLKEAGLLTDLEALGFGIVAFACTTC 479

Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
           NGMSGALDP IQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGT+
Sbjct: 480 NGMSGALDPAIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTV 539

Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
           RFDIEKDVL    DG+P+ LKD+WPSDEEIDA+V  +VKP  +R VYEPMFAI    G  
Sbjct: 540 RFDIEKDVLAV-VDGQPIRLKDLWPSDEEIDAVVKAAVKPAHYRAVYEPMFAIRHDDGPR 598

Query: 601 VSPLYDWRPQSTYIRRPPYWE----GALAGE-RTLKALRPLAVLGDNITTDHLSPSNAIM 655
           VSP YDWRPQSTYIRRPPYW+    GALA   RTL+ +RPLA+L DNITTDHLSPSNAI+
Sbjct: 599 VSPQYDWRPQSTYIRRPPYWDTEGIGALAAHPRTLQGMRPLALLPDNITTDHLSPSNAIL 658

Query: 656 LNSAAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLAR 715
            +SAAGEYLARMGLPEEDFNSYATHRGDHLTA RATFANP L+NEMAVVDG+V+KGSLAR
Sbjct: 659 PDSAAGEYLARMGLPEEDFNSYATHRGDHLTALRATFANPQLVNEMAVVDGKVQKGSLAR 718

Query: 716 IEPEGKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFER 775
           +EPEG+V+RMWEAIETY+ R+QPLIIIAGADYGQGSSRDWAAKGVRLAGVEV+VAEGFER
Sbjct: 719 VEPEGQVMRMWEAIETYLHRRQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVVVAEGFER 778

Query: 776 IHRTNLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVP 835
           IHRTNLIGMGVLPLEF+ GVNR TL L+GTE Y V G+ +P AT+TLVV RK GE V+VP
Sbjct: 779 IHRTNLIGMGVLPLEFEAGVNRTTLQLEGTEVYGVEGDLKPGATVTLVVQRKLGEVVKVP 838

Query: 836 VTCRLDSDEEVSIYEAGGVL-HFAQDFLESSRATA 869
           + CRLD+ EEVS+YEAGGVL  FAQDFL +    A
Sbjct: 839 MRCRLDTAEEVSVYEAGGVLQRFAQDFLAARAGAA 873


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: 2236
Number of extensions: 92
Number of successful extensions: 4
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: 889
Length adjustment: 43
Effective length of query: 826
Effective length of database: 846
Effective search space:   698796
Effective search space used:   698796
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