Alignments for a candidate for acn in Pseudomonas benzenivorans DSM 8628

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Pseudomonas benzenivorans DSM 8628

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 WP_090438007.1 BLS63_RS00030 aconitate hydratase AcnA

Query= SwissProt::Q8ZP52
         (891 letters)



>NCBI__GCF_900100495.1:WP_090438007.1
          Length = 913

 Score = 1221 bits (3158), Expect = 0.0
 Identities = 607/900 (67%), Positives = 720/900 (80%), Gaps = 21/900 (2%)

Query: 12  TLQAKDKTYHYYSLPLAAKSLGDIARLPKSLKVLLENLLRWQDGESVTDEDIQALAGWLK 71
           +L+   +TY Y+SL  AAK+LG++ +LP SLKVLLENLLRW+DG +V   D++A+A WLK
Sbjct: 12  SLEVDGQTYEYFSLAEAAKTLGNLDKLPMSLKVLLENLLRWEDGTTVGGADLRAMADWLK 71

Query: 72  NAHADREIAWRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTSKVNPLSPVDLVIDHSV 131
           +  ++REI +RPARVLMQDFTGVPAVVDLAAMREA+ + GGD  K+NPLSPVDLVIDHSV
Sbjct: 72  SRGSEREIQYRPARVLMQDFTGVPAVVDLAAMREAMAKAGGDPQKINPLSPVDLVIDHSV 131

Query: 132 TVDHFGDDDAFEENVRLEMERNHERYMFLKWGKQAFSRFSVVPPGTGICHQVNLEYLGKA 191
            VD F    AF +NV +EM+RN ERY FL+WG+ AF+ F VVPPGTGICHQVNLEYLG+ 
Sbjct: 132 MVDKFASSAAFGDNVAIEMQRNGERYAFLRWGQHAFANFRVVPPGTGICHQVNLEYLGRT 191

Query: 192 VWSELQDGEWIAYPDSLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPDVVG 251
           VW++ +DG+ +A+PD+LVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIP+V+G
Sbjct: 192 VWTQEEDGQTLAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVIG 251

Query: 252 FKLTGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADRATIANMSPEYG 311
           FKLTGKL+EGITATDLVLTVTQMLR  GVVGKFVEFYGDGL  LPLADRATIANM+PEYG
Sbjct: 252 FKLTGKLKEGITATDLVLTVTQMLRSKGVVGKFVEFYGDGLADLPLADRATIANMAPEYG 311

Query: 312 ATCGFFPIDAITLEYMRLSGRSDDLVELVETYAKAQGMWRNPGDEPVFTSTLELDMGDVE 371
           ATCGFFP+DAITL Y+RLSGR +  V+LVE Y KAQG+WR  G EP+F+ +LELD+G VE
Sbjct: 312 ATCGFFPVDAITLGYLRLSGRPEQSVKLVEAYCKAQGLWRETGFEPLFSDSLELDLGSVE 371

Query: 372 ASLAGPKRPQDRVALGDVPKAFAASAELELNTAQRDRQ-------------------PVD 412
           ASLAGPKRPQDRVAL  V +AF     L++     D                      VD
Sbjct: 372 ASLAGPKRPQDRVALSQVGQAFDEFMGLQVKPNATDEGRLLNEGGGGAAVGSAALVGEVD 431

Query: 413 YTMNGQPYQLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKRQPWVKASLAPG 472
           Y   GQ ++L  GAVVIAAITSCTNTSNPSV+MAAGLLAKKAV  GL R+PWVK+SLAPG
Sbjct: 432 YEHEGQTHRLKHGAVVIAAITSCTNTSNPSVMMAAGLLAKKAVEKGLHRKPWVKSSLAPG 491

Query: 473 SKVVSDYLAQAKLTPYLDELGFNLVGYGCTTCIGNSGPLPEPIETAIKKGDLTVGAVLSG 532
           SKVV+DY   A LT YLDELGF+LVGYGCTTCIGNSGPL EPIE AI++ DLTV +VLSG
Sbjct: 492 SKVVTDYFKAAGLTRYLDELGFDLVGYGCTTCIGNSGPLLEPIEQAIQQHDLTVASVLSG 551

Query: 533 NRNFEGRIHPLVKTNWLASPPLVVAYALAGNMNINLATDPLGYDRKGDPVYLKDIWPSAQ 592
           NRNFEGR+HPLVKTNWLASPPLVVAYALAG++ +N+A +PLG+ + G  VYLKDIWPS +
Sbjct: 552 NRNFEGRVHPLVKTNWLASPPLVVAYALAGSVRMNIAKEPLGHAKDGQAVYLKDIWPSQR 611

Query: 593 EIARAVELVSSDMFRKEYAEVFEGTEEWKSIQVESSDTYGWQSDSTYIRLSPFFDEMQAQ 652
           EIA A++ V + MF KEYAEVF G ++W++IQV  + TY WQ+DSTYI+  PFF+++   
Sbjct: 612 EIAEAMQKVDTAMFHKEYAEVFAGDQQWQAIQVPQAATYAWQADSTYIQHPPFFEDISEA 671

Query: 653 PAPVKDIHGARILAMLGDSVTTDHISPAGSIKPDSPAGRYLQNHGVERKDFNSYGSRRGN 712
           P  + DIH ARILA+LGDSVTTDHISPAG+IK DSPAGRYL+  GVE +DFNSYGSRRGN
Sbjct: 672 PPHIGDIHQARILALLGDSVTTDHISPAGNIKADSPAGRYLREQGVEPRDFNSYGSRRGN 731

Query: 713 HEVMMRGTFANIRIRNEMLPGVEGGMTRHLPGTEAMSIYDAAMLYQQEKTPLAVIAGKEY 772
           HEVMMRGTFANIRIRNEML G EGG T H+P  E +SI++AAM YQ+  TPL V+AGKEY
Sbjct: 732 HEVMMRGTFANIRIRNEMLGGEEGGNTLHVPSGEKLSIFEAAMRYQEAGTPLLVVAGKEY 791

Query: 773 GSGSSRDWAAKGPRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVTRKTLGLTGEEV 832
           G+GSSRDWAAKG  LLG++ VIAESFERIHRSNL+GMG+LPL+F  G  R+TL LTG+E 
Sbjct: 792 GTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFKAGQDRQTLRLTGQET 851

Query: 833 IDIADLQ--NLRPGATIPVTLTRSDGSKETVPCRCRIDTATELTYYQNDGILHYVIRNML 890
           + I  L    L P   + V + R DGS+++    CRIDT  E+ Y++  GILHYV+R ++
Sbjct: 852 LGIYGLDGVELHPHMNLTVEVARVDGSRDSFEVLCRIDTLNEVEYFKAGGILHYVLRQLI 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: 2169
Number of extensions: 95
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: 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 24 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