GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo3_N2E3:AO353_00565
          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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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:

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