GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acnD in Pseudomonas fluorescens FW300-N2E3

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate AO353_00565 AO353_00565 aconitate hydratase

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_00565
          Length = 916

 Score =  722 bits (1863), Expect = 0.0
 Identities = 409/904 (45%), Positives = 556/904 (61%), Gaps = 68/904 (7%)

Query: 20  YFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLT-ASLKQII----ESKQELDF 74
           YF   EA +++  G   KLP + +VL ENL+R  + + +T A LK +     E + + + 
Sbjct: 22  YFSLPEAAKSL--GDLDKLPMSLKVLLENLLRWEDEKTVTGADLKALAAWLKERRSDREI 79

Query: 75  PWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFD 134
            + PARV+  D  G  A+VDLA +R A+A  GGDP ++NP+ P  L++DHS+ V+     
Sbjct: 80  QYRPARVLMQDFTGVPAVVDLAAMRAAMAKAGGDPQRINPLSPVDLVIDHSVMVDKFA-S 138

Query: 135 KDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARNG- 193
             AF +N  IE +RN +R+ F+ W Q AF N  V+P G GI HQ+NLE +   +  ++  
Sbjct: 139 STAFTQNVDIEMQRNGERYAFLRWGQSAFDNFSVVPPGTGICHQVNLEYLGRTVWTKDED 198

Query: 194 ---VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKP 250
               AFPDTLVGTDSHT  ++ LGV+  GVGG+EAE+ MLG+   M +P++IG +LTGK 
Sbjct: 199 DRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVIGFKLTGKL 258

Query: 251 QPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFY 310
           + GITATD+VL +T+ LR + VV  ++EF+G+G   L L DRATI+NM PE+GAT   F 
Sbjct: 259 KEGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLAELPLADRATIANMAPEYGATCGFFP 318

Query: 311 IDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPS 370
           +D+ TL+YL L+GR +  VKLVE Y KT GLW    ++ V+  +L  D+SSV  ++AGP 
Sbjct: 319 VDEVTLEYLRLSGRPSAVVKLVEAYCKTQGLWRLPGQEPVFTDSLALDMSSVEASLAGPK 378

Query: 371 NPHARV---------------------PTSE----LAARGISG--------------EVE 391
            P  RV                     PTS+    L + G  G              E E
Sbjct: 379 RPQDRVSLPNVAQAFTDFLGLQVKPARPTSKEEGRLESEGGGGVAVGNADLVSEADYEYE 438

Query: 392 NEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAV 451
            +   + +GAV+IAAITSCTNTSNP  ++AAGL+A+ A  KGL RKPWVK+SLAPGSK V
Sbjct: 439 GQTYRLKNGAVVIAAITSCTNTSNPSVMMAAGLVAKKAVEKGLKRKPWVKSSLAPGSKVV 498

Query: 452 QLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNF 511
             Y + A L   L+ LGF +VG+ CTTC G SG L   I++ +   DL   +VLSGNRNF
Sbjct: 499 TDYYKAAGLTQYLDELGFSLVGYGCTTCIGNSGPLLEPIEKAIQSSDLAVASVLSGNRNF 558

Query: 512 DGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEI-D 570
           +GR+HP  K  +LASPPLVVAYA+AG++R DI  + LG  KDGKPV L +IWPS  EI D
Sbjct: 559 EGRVHPLVKTNWLASPPLVVAYALAGSVRMDISSEPLGEGKDGKPVYLRDIWPSSKEIAD 618

Query: 571 AVIAASVKPEQFRKVYEPMFDLSVDYGDKVSP---LYDWRPQSTYIRRPPYWE---GALA 624
           AV  A V    F K Y  +F     +     P    Y W+  STYI+ PP+++   G L 
Sbjct: 619 AV--AQVDTAMFHKEYAEVFAGDAQWQAIEVPQAATYVWQKDSTYIQHPPFFDDISGPLP 676

Query: 625 GERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHL 684
             + + G R LA+LGD++TTDH+SP+  I  DS AG YL + G+   DFNSY + RG+H 
Sbjct: 677 VIQDISGARILALLGDSVTTDHISPAGNIKADSPAGRYLREQGVEPRDFNSYGSRRGNHE 736

Query: 685 TAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGA 744
              R TFAN +++NEM    G  + G+   I P G    +++A   Y     PL++IAG 
Sbjct: 737 VMMRGTFANIRIRNEML---GGEEGGNTLYI-PTGEKLAIYDAAMRYQAAGTPLVVIAGQ 792

Query: 745 DYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGT 804
           +YG GSSRDWAAKG  L GV+A++AE FERIHR+NLVGMGVLPL+FK  +NR +  + G 
Sbjct: 793 EYGTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFKLDQNRKSLNLTGK 852

Query: 805 EVFDVIG----SIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQD 860
           E  D+ G     + PR +LT++ITR++G   +V V CR+DT  EV  ++AGG+L    + 
Sbjct: 853 ETLDIQGLTGVELTPRMNLTLVITREDGSSEKVEVLCRIDTLNEVEYFKAGGILHYVLRQ 912

Query: 861 FLES 864
            + S
Sbjct: 913 LIAS 916


Lambda     K      H
   0.318    0.136    0.397 

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: 1961
Number of extensions: 94
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 867
Length of database: 916
Length adjustment: 43
Effective length of query: 824
Effective length of database: 873
Effective search space:   719352
Effective search space used:   719352
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 (21.7 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