Alignments for a candidate for acn in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Pseudomonas simiae WCS417

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 GFF1478 PS417_07515 aconitate hydratase

Query= SwissProt::Q8ZP52
         (891 letters)



>FitnessBrowser__WCS417:GFF1478
          Length = 913

 Score = 1250 bits (3234), Expect = 0.0
 Identities = 621/911 (68%), Positives = 730/911 (80%), Gaps = 21/911 (2%)

Query: 1   MSSTLREASKDTLQAKDKTYHYYSLPLAAKSLGDIARLPKSLKVLLENLLRWQDGESVTD 60
           MSS     +  TL+   KTYHY+SLP AAKSLGD+ +LP SLKVLLENLLRW+D ++VT 
Sbjct: 1   MSSLDSLRTLKTLEIDSKTYHYFSLPEAAKSLGDLDKLPMSLKVLLENLLRWEDNKTVTG 60

Query: 61  EDIQALAGWLKNAHADREIAWRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTSKVNPL 120
            D++A+A WLK   +DREI +RPARVLMQDFTGVPAVVDLAAMR AV + GGD  ++NPL
Sbjct: 61  ADLKAIAAWLKERQSDREIQYRPARVLMQDFTGVPAVVDLAAMRAAVAKAGGDPQRINPL 120

Query: 121 SPVDLVIDHSVTVDHFGDDDAFEENVRLEMERNHERYMFLKWGKQAFSRFSVVPPGTGIC 180
           SPVDLVIDHSV VD FG   AFE+NV +EM+RN ERY FL+WG+ AF  FSVVPPGTGIC
Sbjct: 121 SPVDLVIDHSVMVDKFGTTGAFEQNVDIEMQRNGERYAFLRWGQSAFDNFSVVPPGTGIC 180

Query: 181 HQVNLEYLGKAVWSELQDGEWIAYPDSLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 240
           HQVNLEYLG+ VW++ +DG   A+PD+LVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ
Sbjct: 181 HQVNLEYLGRTVWTKDEDGRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 240

Query: 241 PVSMLIPDVVGFKLTGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADR 300
           PVSMLIP+V+GFKLTGKL+EGITATDLVLTVTQMLRK GVVGKFVEFYGDGL  LPLADR
Sbjct: 241 PVSMLIPEVIGFKLTGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLADLPLADR 300

Query: 301 ATIANMSPEYGATCGFFPIDAITLEYMRLSGRSDDLVELVETYAKAQGMWRNPGDEPVFT 360
           ATIANM+PEYGATCGFFP+D +TL+Y+RLSGR  + V+LVE Y KAQG+WRN G EPVFT
Sbjct: 301 ATIANMAPEYGATCGFFPVDEVTLDYLRLSGRPTETVKLVEAYTKAQGLWRNAGQEPVFT 360

Query: 361 STLELDMGDVEASLAGPKRPQDRVALGDVPKAFAASAELELNTAQRDRQPV--------- 411
            +L LDMG VEASLAGPKRPQDRVAL +V +AF+   +L+     ++   +         
Sbjct: 361 DSLALDMGSVEASLAGPKRPQDRVALPNVGQAFSDFLDLQFKPTNKEEGRLESEGGGGVA 420

Query: 412 ----------DYTMNGQPYQLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKR 461
                     DY  +GQ Y+L +GAVVIAAITSCTNTSNPSV+MAAGLLAKKAV  GL R
Sbjct: 421 VGNADLVGETDYEYDGQTYRLKNGAVVIAAITSCTNTSNPSVMMAAGLLAKKAVEKGLTR 480

Query: 462 QPWVKASLAPGSKVVSDYLAQAKLTPYLDELGFNLVGYGCTTCIGNSGPLPEPIETAIKK 521
           +PWVK SLAPGSKVV+DY   A LT YLD+LGF+LVGYGCTTCIGNSGPLPEPIE AI+K
Sbjct: 481 KPWVKTSLAPGSKVVTDYYKAAGLTQYLDKLGFDLVGYGCTTCIGNSGPLPEPIEKAIQK 540

Query: 522 GDLTVGAVLSGNRNFEGRIHPLVKTNWLASPPLVVAYALAGNMNINLATDPLGYDRKGDP 581
            DL V +VLSGNRNFEGR+HPLVKTNWLASPPLVVAYALAG + I+++++PLG D+ G P
Sbjct: 541 ADLAVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGTVRIDISSEPLGNDQHGHP 600

Query: 582 VYLKDIWPSAQEIARAVELVSSDMFRKEYAEVFEGTEEWKSIQVESSDTYGWQSDSTYIR 641
           VYLKDIWP++QEIA AV  V++ MF KEYAEVF G E+W++I+V  + TY WQ DSTYI+
Sbjct: 601 VYLKDIWPTSQEIADAVAQVTTGMFHKEYAEVFAGDEQWQAIEVPQAATYVWQKDSTYIQ 660

Query: 642 LSPFFDEMQAQPAPVKDIHGARILAMLGDSVTTDHISPAGSIKPDSPAGRYLQNHGVERK 701
             PFFD++      +KD+ GA +LA+LGDSVTTDHISPAG+IK DSPAGRYL+  GVE +
Sbjct: 661 HPPFFDDIAGPLPVIKDVKGANVLALLGDSVTTDHISPAGNIKTDSPAGRYLREQGVEPR 720

Query: 702 DFNSYGSRRGNHEVMMRGTFANIRIRNEMLPGVEGGMTRHLPGTEAMSIYDAAMLYQQEK 761
           DFNSYGSRRGNHEVMMRGTFANIRIRNEML G EGG T ++P  E M IYDA+M YQ   
Sbjct: 721 DFNSYGSRRGNHEVMMRGTFANIRIRNEMLGGEEGGNTLYIPTGEKMPIYDASMKYQASG 780

Query: 762 TPLAVIAGKEYGSGSSRDWAAKGPRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVT 821
           TPL V+AG+EYG+GSSRDWAAKG  LLG++ VIAESFERIHRSNL+GMG+LPL+F     
Sbjct: 781 TPLVVVAGQEYGTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFKLDQN 840

Query: 822 RKTLGLTGEEVIDIADLQNLR--PGATIPVTLTRSDGSKETVPCRCRIDTATELTYYQND 879
           RK+L LTG+E IDI  L ++   P   + + +TR DGS E V   CRIDT  E+ Y+++ 
Sbjct: 841 RKSLKLTGKEKIDILGLTDVEIVPRMNLTLVITREDGSSEKVEVLCRIDTLNEVEYFKSG 900

Query: 880 GILHYVIRNML 890
           GILHYV+R ++
Sbjct: 901 GILHYVLRQLI 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: 2203
Number of extensions: 90
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 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