Alignments for a candidate for acn in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Pseudomonas putida KT2440

Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; 2-methyl-cis-aconitate hydratase; Iron-responsive protein-like; IRP-like; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate PP_2112 PP_2112 aconitate hydratase 1

Query= SwissProt::Q8ZP52
         (891 letters)



>FitnessBrowser__Putida:PP_2112
          Length = 913

 Score = 1252 bits (3239), Expect = 0.0
 Identities = 621/899 (69%), Positives = 720/899 (80%), Gaps = 21/899 (2%)

Query: 13  LQAKDKTYHYYSLPLAAKSLGDIARLPKSLKVLLENLLRWQDGESVTDEDIQALAGWLKN 72
           L+  DKTYHY+SL  AA+ LGD+ RLP SLKVLLENLLRW+DG +VT +D++A+A WL  
Sbjct: 13  LKVGDKTYHYFSLTEAARQLGDLQRLPMSLKVLLENLLRWEDGATVTGDDLRAIAQWLGE 72

Query: 73  AHADREIAWRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTSKVNPLSPVDLVIDHSVT 132
             +DREI +RPARVLMQDFTGVPAVVDLAAMR A+ + GGD  ++NPLSPVDLVIDHSV 
Sbjct: 73  RRSDREIQYRPARVLMQDFTGVPAVVDLAAMRAAMAKAGGDPQRINPLSPVDLVIDHSVM 132

Query: 133 VDHFGDDDAFEENVRLEMERNHERYMFLKWGKQAFSRFSVVPPGTGICHQVNLEYLGKAV 192
           VD +G   AF ENV +EM+RN ERY FL+WG+ AF  F VVPPGTGICHQVNLEYLG+ V
Sbjct: 133 VDRYGTPQAFAENVDIEMQRNGERYAFLRWGQSAFDNFRVVPPGTGICHQVNLEYLGRTV 192

Query: 193 WSELQDGEWIAYPDSLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPDVVGF 252
           W+   DG   A+PD+LVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIP+V+GF
Sbjct: 193 WTREADGRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVIGF 252

Query: 253 KLTGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADRATIANMSPEYGA 312
           KLTGKLREGITATDLVLTVTQMLRK GVVGKFVEFYGDGL  LPLADRATIANM+PEYGA
Sbjct: 253 KLTGKLREGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLAELPLADRATIANMAPEYGA 312

Query: 313 TCGFFPIDAITLEYMRLSGRSDDLVELVETYAKAQGMWRNPGDEPVFTSTLELDMGDVEA 372
           TCGFFP+D +TL+Y+RLSGR +  V+LVE Y KAQGMWR PG EP F+ TL LDM DVEA
Sbjct: 313 TCGFFPVDQVTLDYLRLSGRPEATVQLVEQYCKAQGMWRLPGQEPSFSDTLALDMDDVEA 372

Query: 373 SLAGPKRPQDRVALGDVPKAFAASAELELNTAQRD-------------------RQPVDY 413
           SLAGPKRPQDRVALG V +AF    EL+     ++                      VDY
Sbjct: 373 SLAGPKRPQDRVALGQVSQAFDHFIELQPKPLAKEVGRLESEGGGGVAVGNADQTGAVDY 432

Query: 414 TMNGQPYQLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKRQPWVKASLAPGS 473
           +  GQ + L DGAVVIAAITSCTNTSNPSV+MAAGL+AKKA+  GL+R+PWVK+SLAPGS
Sbjct: 433 SHQGQTHTLRDGAVVIAAITSCTNTSNPSVMMAAGLVAKKALEKGLQRKPWVKSSLAPGS 492

Query: 474 KVVSDYLAQAKLTPYLDELGFNLVGYGCTTCIGNSGPLPEPIETAIKKGDLTVGAVLSGN 533
           KVV+DY   A LTPYLD+LGF+LVGYGCTTCIGNSGPL E IE AI   DLTV +VLSGN
Sbjct: 493 KVVTDYFKAAGLTPYLDQLGFDLVGYGCTTCIGNSGPLDEAIEKAIGSADLTVASVLSGN 552

Query: 534 RNFEGRIHPLVKTNWLASPPLVVAYALAGNMNINLATDPLGYDRKGDPVYLKDIWPSAQE 593
           RNFEGR+HPLVKTNWLASPPLVVAYALAG++ ++L  DPLG  + G PVYL+DIWPS QE
Sbjct: 553 RNFEGRVHPLVKTNWLASPPLVVAYALAGSVRLDLTRDPLGSGKDGQPVYLRDIWPSQQE 612

Query: 594 IARAVELVSSDMFRKEYAEVFEGTEEWKSIQVESSDTYGWQSDSTYIRLSPFFDEMQAQP 653
           IA AV  V + MF KEYAEVF G  +W++I+V  + TY WQ+DSTYI+  PFFD +   P
Sbjct: 613 IAEAVAKVDTAMFHKEYAEVFAGDAQWQAIEVPQAATYVWQADSTYIQHPPFFDGIGGPP 672

Query: 654 APVKDIHGARILAMLGDSVTTDHISPAGSIKPDSPAGRYLQNHGVERKDFNSYGSRRGNH 713
             + +IHGAR+LA+LGDSVTTDHISPAG+IK DSPAGRYL+  GVE +DFNSYGSRRGNH
Sbjct: 673 PQIANIHGARVLALLGDSVTTDHISPAGNIKTDSPAGRYLREQGVEPRDFNSYGSRRGNH 732

Query: 714 EVMMRGTFANIRIRNEMLPGVEGGMTRHLPGTEAMSIYDAAMLYQQEKTPLAVIAGKEYG 773
           EVMMRGTFANIRIRNEML G EGG T H+P  E +SIYDAAM YQQE TPL VIAG+EYG
Sbjct: 733 EVMMRGTFANIRIRNEMLAGEEGGNTLHVPTGEKLSIYDAAMRYQQEGTPLLVIAGQEYG 792

Query: 774 SGSSRDWAAKGPRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVTRKTLGLTGEEVI 833
           +GSSRDWAAKG  LLG++ V+AESFERIHRSNL+GMG+LPL+F  G  RK LGLTG+E I
Sbjct: 793 TGSSRDWAAKGTNLLGVKAVLAESFERIHRSNLVGMGVLPLQFKAGHNRKQLGLTGKEQI 852

Query: 834 DIADLQ--NLRPGATIPVTLTRSDGSKETVPCRCRIDTATELTYYQNDGILHYVIRNML 890
           D+  L   ++ PG ++P+ +TR DG +E +   CRIDT  E+ Y++  GILHYV+R M+
Sbjct: 853 DVLGLDGAHIHPGMSLPLRITREDGQQEQIEVLCRIDTLNEVEYFKAGGILHYVLRQMI 911


Lambda     K      H
   0.317    0.135    0.401 

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: 2250
Number of extensions: 96
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: 891
Length of database: 913
Length adjustment: 43
Effective length of query: 848
Effective length of database: 870
Effective search space:   737760
Effective search space used:   737760
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: 56 (26.2 bits)

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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