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; ACN; 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_1140 Aconitate hydratase (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (EC 4.2.1.99)

Query= SwissProt::O53166
         (943 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1140
          Length = 980

 Score =  922 bits (2384), Expect = 0.0
 Identities = 484/960 (50%), Positives = 639/960 (66%), Gaps = 47/960 (4%)

Query: 20  KSYQIYRLDAV----PNTAKLPYSLKVLAENLLRNEDGSNITKDHIEAIANWDPKAEPSI 75
           K  Q Y L A+    P   +LP S++++ E++LRN DG  +T +H+E +A W P AE   
Sbjct: 29  KDGQFYSLPALAKQFPEIKRLPVSIRIVLESVLRNCDGRKVTPEHVEQLARWAPNAERKD 88

Query: 76  EIQYTPARVVMQDFTGVPCIVDLATMREAIADLGGNPDKVNPLAPADLVIDHSVIADLFG 135
           EI +  +RVV+QDFTGVP + DLA MR   A LG NP K+ PL P DLV+DHS++ D +G
Sbjct: 89  EIPFVVSRVVLQDFTGVPLLADLAAMRSVAAKLGKNPKKIEPLVPVDLVVDHSIMIDHYG 148

Query: 136 RADAFERNVEIEYQRNGERYQFLRWGQGAFDDFKVVPPGTGIVHQVNIEYLASVVMTR-D 194
           + ++ + N+++E+QRN ERY+F++WG  AFD F VVPPG GIVHQVN+EYLA  V  R D
Sbjct: 149 KKNSLDLNMKLEFQRNRERYEFMKWGMQAFDTFGVVPPGFGIVHQVNLEYLARGVHKRKD 208

Query: 195 GVAYPDTCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSMLIPRVVGFRLTGEIQP 254
           GV YPDT VGTDSHTTM+NG+GV+GWGVGGIEAEAAMLGQPV  L P VVGF +TG ++ 
Sbjct: 209 GVFYPDTLVGTDSHTTMINGIGVVGWGVGGIEAEAAMLGQPVYFLTPDVVGFEMTGRLRE 268

Query: 255 GVTATDVVLTVTEMLRQHGVVGKFVEFYGEGVAEVPLANRATLGNMSPEFGSTAAIFPID 314
           GVTATD+VLTVTE+LR+H VVGKFVEF+GEG   + L +RAT+GNM+PE+G+T   FP+D
Sbjct: 269 GVTATDLVLTVTELLRKHKVVGKFVEFFGEGTRTLALPDRATIGNMAPEYGATMGFFPVD 328

Query: 315 EETIKYLRFTGRTPEQVALVEAYAKAQGMWHDP-KHEPEFSEYLELNLSDVVPSIAGPKR 373
           E+TI Y + TGRT  ++   EAY KAQG++  P   E ++S+ + L+L  V PS+AGPKR
Sbjct: 329 EKTIDYFQGTGRTKAEIEAFEAYFKAQGLFGVPLAGEVDYSQVVTLDLGSVTPSLAGPKR 388

Query: 374 PQDRIALAQAKSTFREQIYHYVGNGSPDSPHDP-HSKLD-----EVVEETFPASDPGQLT 427
           PQDRI L Q    F +       +   + P +  H++       EVV +  P   P    
Sbjct: 389 PQDRIELGQVSRQFADLFSQPAAHNGFNRPAELLHTRFHIHRAAEVVADVTPDGKPTPAG 448

Query: 428 FANDDVATDETVHS-AAAHADGRVSN-PVRVKSDELGEFVLDHGAVVIAAITSCTNTSNP 485
                V  +    + A AHA+ R +  P R     +G     +G V+IAAITSCTNTSNP
Sbjct: 449 APRSVVEMEANKPALATAHAEARSATLPARGADPTVG-----NGDVLIAAITSCTNTSNP 503

Query: 486 EVMLGAALLARNAVEKGLTSKPWVKTTIAPGSQVVNDYYDRSGLWPYLEKLGFYLVGYGC 545
            V+L A LLA+ AVE GL  +P +KT++APGS++V +Y   +GL PYLEKLGF + GYGC
Sbjct: 504 SVLLAAGLLAKKAVEAGLKVQPHIKTSLAPGSRIVTEYLSETGLLPYLEKLGFSIAGYGC 563

Query: 546 TTCIGNSGPLPEEISKAVNDNDLSVTAVLSGNRNFEGRINPDVKMNYLASPPLVIAYALA 605
           TTCIGN+G L  E+++A+  NDL   AVLSGNRNFE RI+P++K N+LASPPLV+AYA+A
Sbjct: 564 TTCIGNAGDLTPELNEAITQNDLVCAAVLSGNRNFEARIHPNLKANFLASPPLVVAYAIA 623

Query: 606 GTMDFDFQTQPLGQDKDGKNVFLRDIWPSQQDVSDTIAAAINQEMFTRNYADVFKGDDR- 664
           GT+  D  T+P+GQ K GK+++L DIWPS  +V   +  A+  + F  NYA V     + 
Sbjct: 624 GTVLKDLMTEPVGQGKGGKDIYLGDIWPSSDEVHALLKFAMKGKAFRDNYAKVATDPGKL 683

Query: 665 WRNLPTPSGNTFEWDPNSTYVRKPPYF---------------EGMTAKPEPVGNISGARV 709
           W  +   SG  + W P STY+ +PP+F                G   K   + ++ GAR+
Sbjct: 684 WEKIQGVSGTAYTW-PASTYIAEPPFFAQFALEKGANKASGTRGEGQKDAQLPSVMGARI 742

Query: 710 LALLGDSVTTDHISPAGAIKPGTPAARYLDEHGVDRKDYNSFGSRRGNHEVMIRGTFANI 769
           +AL GDS+TTDHISPAG+IK  +PA ++L +HGV + D+NS+G+RRGNH+VM+RGTFAN+
Sbjct: 743 MALFGDSITTDHISPAGSIKESSPAGQWLLQHGVQKADFNSYGARRGNHDVMVRGTFANV 802

Query: 770 RLRNQLLDDVSGGYTRD-----FTQPG---GPQAFIYDAAQNYAAQHIPLVVFGGKEYGS 821
           R++N ++   + G   +     F   G   G + FI+DAA  Y AQ  P VVF G+EYG+
Sbjct: 803 RIKNLMIPPTADGSREEGGVTVFQNEGALQGEKMFIFDAAMQYMAQGTPTVVFAGEEYGT 862

Query: 822 GSSRDWAAKGTLLLGVRAVIAESFERIHRSNLIGMGVIPLQFPEGKSASSLGLDGTEVFD 881
           GSSRDWAAKGT LLG++AV+A SFERIHRSNL+GMGV+PLQF  G S  +LGL G EV D
Sbjct: 863 GSSRDWAAKGTQLLGIKAVVARSFERIHRSNLVGMGVLPLQFKAGDSWETLGLTGNEVID 922

Query: 882 ITGIDVLNDGKTPKTVCVQATKGDGATIEFDAVVRIDTPGEADYYRNGGILQYVLRNILK 941
           +     L      + V  +A   DG   E    +RIDTP E DYYR GGIL +VLR +L+
Sbjct: 923 VLPDPALTPQSDARLVIRRA---DGTVREVVVTLRIDTPIEVDYYRAGGILPFVLRQLLE 979


Lambda     K      H
   0.316    0.136    0.403 

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: 2464
Number of extensions: 123
Number of successful extensions: 8
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: 943
Length of database: 980
Length adjustment: 44
Effective length of query: 899
Effective length of database: 936
Effective search space:   841464
Effective search space used:   841464
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 (21.6 bits)
S2: 57 (26.6 bits)

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

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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