GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_3888 Aconitate hydratase (EC 4.2.1.3)

Query= SwissProt::Q8ZP52
         (891 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 Aconitate hydratase
           (EC 4.2.1.3)
          Length = 913

 Score = 1241 bits (3211), Expect = 0.0
 Identities = 614/900 (68%), Positives = 723/900 (80%), Gaps = 21/900 (2%)

Query: 12  TLQAKDKTYHYYSLPLAAKSLGDIARLPKSLKVLLENLLRWQDGESVTDEDIQALAGWLK 71
           TLQ  DKTYHY+SLP AAKSLGD+ +LP SLKVLLENLLRW+D ++VT  D++A+A WLK
Sbjct: 12  TLQVDDKTYHYFSLPEAAKSLGDLDKLPMSLKVLLENLLRWEDEKTVTGADLKAIAAWLK 71

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

Query: 132 TVDHFGDDDAFEENVRLEMERNHERYMFLKWGKQAFSRFSVVPPGTGICHQVNLEYLGKA 191
            VD +    AF +NV +EM+RNHERY FL+WG+ AF+ FSVVPPGTGICHQVNLEYLG+ 
Sbjct: 132 MVDKYASASAFGQNVDIEMQRNHERYAFLRWGQSAFNNFSVVPPGTGICHQVNLEYLGRT 191

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

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

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

Query: 372 ASLAGPKRPQDRVALGDVPKAFAASAELELNTAQRDRQPV-------------------D 412
           ASLAGPKRPQDRV+L +V +AF     L+   + ++   +                   D
Sbjct: 372 ASLAGPKRPQDRVSLPNVAQAFTDFLGLQFKPSSKEEGRLESEGGGGVAVGNADLIGEAD 431

Query: 413 YTMNGQPYQLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKRQPWVKASLAPG 472
           Y   G  Y+L +GAVVIAAITSCTNTSNPSV+MAAGL+AKKAV  GLKR+PWVK+SLAPG
Sbjct: 432 YHHEGSTYRLKNGAVVIAAITSCTNTSNPSVMMAAGLVAKKAVEKGLKRKPWVKSSLAPG 491

Query: 473 SKVVSDYLAQAKLTPYLDELGFNLVGYGCTTCIGNSGPLPEPIETAIKKGDLTVGAVLSG 532
           SKVV+DY   A LT YLDELGF LVGYGCTTCIGNSGPLPEPIE AI+K DLTV +VLSG
Sbjct: 492 SKVVTDYYKAAGLTQYLDELGFALVGYGCTTCIGNSGPLPEPIEKAIQKADLTVASVLSG 551

Query: 533 NRNFEGRIHPLVKTNWLASPPLVVAYALAGNMNINLATDPLGYDRKGDPVYLKDIWPSAQ 592
           NRNFEGR+HPLVKTNWLASPPLVVAYALAG + I+++++PLG D+ G PVYL+DIWPS +
Sbjct: 552 NRNFEGRVHPLVKTNWLASPPLVVAYALAGTVRIDISSEPLGNDKDGHPVYLRDIWPSTK 611

Query: 593 EIARAVELVSSDMFRKEYAEVFEGTEEWKSIQVESSDTYGWQSDSTYIRLSPFFDEMQAQ 652
           EIA AV  V++ MF KEYAEVF G E+W++I+V  + TY W +DSTYI+  PFFD++   
Sbjct: 612 EIADAVTQVNTAMFHKEYAEVFAGDEQWQAIEVPQAATYVWNNDSTYIQHPPFFDDIGGP 671

Query: 653 PAPVKDIHGARILAMLGDSVTTDHISPAGSIKPDSPAGRYLQNHGVERKDFNSYGSRRGN 712
              VKD+ GA++LA+LGDSVTTDHISPAG+IK DSPAG YL+  GVE +DFNSYGSRRGN
Sbjct: 672 APVVKDVEGAKVLALLGDSVTTDHISPAGNIKADSPAGHYLREQGVEPRDFNSYGSRRGN 731

Query: 713 HEVMMRGTFANIRIRNEMLPGVEGGMTRHLPGTEAMSIYDAAMLYQQEKTPLAVIAGKEY 772
           H+VMMRGTFANIRIRNEML G EGG T ++P  E + IYDAAM YQ   TPL VIAG+EY
Sbjct: 732 HQVMMRGTFANIRIRNEMLGGEEGGNTIYIPTGEKLPIYDAAMRYQASGTPLVVIAGQEY 791

Query: 773 GSGSSRDWAAKGPRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVTRKTLGLTGEEV 832
           G+GSSRDWAAKG  LLG++ VIAESFERIHRSNL+GMG+LPL+F     RK+L LTG+E 
Sbjct: 792 GTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFKLDQNRKSLNLTGKET 851

Query: 833 IDIADLQ--NLRPGATIPVTLTRSDGSKETVPCRCRIDTATELTYYQNDGILHYVIRNML 890
           +DI  L    L P   + + +TR DG+ E V   CRIDT  E+ Y++  GILHYV+R ++
Sbjct: 852 LDILGLTGVELTPRMNLTLVVTREDGNTEKVEVLCRIDTLNEVEYFKAGGILHYVLRQLI 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: 2211
Number of extensions: 94
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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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:

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:

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:

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, 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