Aligments for a candidate for acn in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Aligments for a candidate for acn in Pseudomonas fluorescens FW300-N2E3

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 AO353_00565 AO353_00565 aconitate hydratase

Query= SwissProt::Q8ZP52
         (891 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 AO353_00565 aconitate
           hydratase
          Length = 916

 Score = 1228 bits (3178), Expect = 0.0
 Identities = 613/903 (67%), Positives = 718/903 (79%), Gaps = 24/903 (2%)

Query: 12  TLQAKDKTYHYYSLPLAAKSLGDIARLPKSLKVLLENLLRWQDGESVTDEDIQALAGWLK 71
           TL+  DKTYHY+SLP AAKSLGD+ +LP SLKVLLENLLRW+D ++VT  D++ALA WLK
Sbjct: 12  TLKIDDKTYHYFSLPEAAKSLGDLDKLPMSLKVLLENLLRWEDEKTVTGADLKALAAWLK 71

Query: 72  NAHADREIAWRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTSKVNPLSPVDLVIDHSV 131
              +DREI +RPARVLMQDFTGVPAVVDLAAMR A+ + GGD  ++NPLSPVDLVIDHSV
Sbjct: 72  ERRSDREIQYRPARVLMQDFTGVPAVVDLAAMRAAMAKAGGDPQRINPLSPVDLVIDHSV 131

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

Query: 192 VWSELQDGEWIAYPDSLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPDVVG 251
           VW++ +D    A+PD+LVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIP+V+G
Sbjct: 192 VWTKDEDDRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVIG 251

Query: 252 FKLTGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADRATIANMSPEYG 311
           FKLTGKL+EGITATDLVLTVTQMLRK GVVGKFVEFYGDGL  LPLADRATIANM+PEYG
Sbjct: 252 FKLTGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLAELPLADRATIANMAPEYG 311

Query: 312 ATCGFFPIDAITLEYMRLSGRSDDLVELVETYAKAQGMWRNPGDEPVFTSTLELDMGDVE 371
           ATCGFFP+D +TLEY+RLSGR   +V+LVE Y K QG+WR PG EPVFT +L LDM  VE
Sbjct: 312 ATCGFFPVDEVTLEYLRLSGRPSAVVKLVEAYCKTQGLWRLPGQEPVFTDSLALDMSSVE 371

Query: 372 ASLAGPKRPQDRVALGDVPKAFAASAELELNTAQRDRQP--------------------- 410
           ASLAGPKRPQDRV+L +V +AF     L++  A+   +                      
Sbjct: 372 ASLAGPKRPQDRVSLPNVAQAFTDFLGLQVKPARPTSKEEGRLESEGGGGVAVGNADLVS 431

Query: 411 -VDYTMNGQPYQLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKRQPWVKASL 469
             DY   GQ Y+L +GAVVIAAITSCTNTSNPSV+MAAGL+AKKAV  GLKR+PWVK+SL
Sbjct: 432 EADYEYEGQTYRLKNGAVVIAAITSCTNTSNPSVMMAAGLVAKKAVEKGLKRKPWVKSSL 491

Query: 470 APGSKVVSDYLAQAKLTPYLDELGFNLVGYGCTTCIGNSGPLPEPIETAIKKGDLTVGAV 529
           APGSKVV+DY   A LT YLDELGF+LVGYGCTTCIGNSGPL EPIE AI+  DL V +V
Sbjct: 492 APGSKVVTDYYKAAGLTQYLDELGFSLVGYGCTTCIGNSGPLLEPIEKAIQSSDLAVASV 551

Query: 530 LSGNRNFEGRIHPLVKTNWLASPPLVVAYALAGNMNINLATDPLGYDRKGDPVYLKDIWP 589
           LSGNRNFEGR+HPLVKTNWLASPPLVVAYALAG++ ++++++PLG  + G PVYL+DIWP
Sbjct: 552 LSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGSVRMDISSEPLGEGKDGKPVYLRDIWP 611

Query: 590 SAQEIARAVELVSSDMFRKEYAEVFEGTEEWKSIQVESSDTYGWQSDSTYIRLSPFFDEM 649
           S++EIA AV  V + MF KEYAEVF G  +W++I+V  + TY WQ DSTYI+  PFFD++
Sbjct: 612 SSKEIADAVAQVDTAMFHKEYAEVFAGDAQWQAIEVPQAATYVWQKDSTYIQHPPFFDDI 671

Query: 650 QAQPAPVKDIHGARILAMLGDSVTTDHISPAGSIKPDSPAGRYLQNHGVERKDFNSYGSR 709
                 ++DI GARILA+LGDSVTTDHISPAG+IK DSPAGRYL+  GVE +DFNSYGSR
Sbjct: 672 SGPLPVIQDISGARILALLGDSVTTDHISPAGNIKADSPAGRYLREQGVEPRDFNSYGSR 731

Query: 710 RGNHEVMMRGTFANIRIRNEMLPGVEGGMTRHLPGTEAMSIYDAAMLYQQEKTPLAVIAG 769
           RGNHEVMMRGTFANIRIRNEML G EGG T ++P  E ++IYDAAM YQ   TPL VIAG
Sbjct: 732 RGNHEVMMRGTFANIRIRNEMLGGEEGGNTLYIPTGEKLAIYDAAMRYQAAGTPLVVIAG 791

Query: 770 KEYGSGSSRDWAAKGPRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVTRKTLGLTG 829
           +EYG+GSSRDWAAKG  LLG++ VIAESFERIHRSNL+GMG+LPL+F     RK+L LTG
Sbjct: 792 QEYGTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFKLDQNRKSLNLTG 851

Query: 830 EEVIDIADLQ--NLRPGATIPVTLTRSDGSKETVPCRCRIDTATELTYYQNDGILHYVIR 887
           +E +DI  L    L P   + + +TR DGS E V   CRIDT  E+ Y++  GILHYV+R
Sbjct: 852 KETLDIQGLTGVELTPRMNLTLVITREDGSSEKVEVLCRIDTLNEVEYFKAGGILHYVLR 911

Query: 888 NML 890
            ++
Sbjct: 912 QLI 914


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: 2201
Number of extensions: 89
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: 916
Length adjustment: 43
Effective length of query: 848
Effective length of database: 873
Effective search space:   740304
Effective search space used:   740304
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.

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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 preprint on GapMind for carbon sources, or view the source code.

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