GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acnD in Pseudomonas fluorescens FW300-N2E2

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate Pf6N2E2_2301 Aconitate hydratase (EC 4.2.1.3)

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2301
          Length = 913

 Score =  730 bits (1884), Expect = 0.0
 Identities = 404/890 (45%), Positives = 549/890 (61%), Gaps = 63/890 (7%)

Query: 20  YFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTAS-LKQII----ESKQELDF 74
           YF   EA  ++  G   KLP + +VL ENL+R  + + +T + LK +     E + + + 
Sbjct: 22  YFSLPEAARSL--GDLDKLPMSLKVLLENLLRWEDEKTVTGTDLKALAGWLKERRSDREI 79

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

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

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

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

Query: 311 IDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPS 370
           +D+ TLDYL L+GR AE VKLVE Y K  GLW    ++ V+  TL  D+ SV  ++AGP 
Sbjct: 319 VDEVTLDYLRLSGRPAETVKLVEAYCKAQGLWRLPGQEPVFTDTLELDMGSVEASLAGPK 378

Query: 371 NPHARV------------------PTSE----LAARGISG--------------EVENEP 394
            P  RV                  PTS+    L + G  G              E E   
Sbjct: 379 RPQDRVSLPNVGQAFSDFLGLQVKPTSKEEGRLESEGGGGVAVGNADQVGEAEYEFEGHT 438

Query: 395 GLMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLY 454
             + +GAV+IAAITSCTNTSNP  ++AAGLLA+ A  KGLTRKPWVK+SLAPGSK V  Y
Sbjct: 439 HRLKNGAVVIAAITSCTNTSNPSVMMAAGLLAKKAVEKGLTRKPWVKSSLAPGSKVVTDY 498

Query: 455 LEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGR 514
            + A L   L+ LGF +VG+ CTTC G SG L   I++ +   DL   +VLSGNRNF+GR
Sbjct: 499 YKAAGLTEYLDKLGFDLVGYGCTTCIGNSGPLPEPIEKAIQKADLTVASVLSGNRNFEGR 558

Query: 515 IHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIA 574
           +HP  K  +LASPPLVVAYA+AGT+R DI  + LG D+DGKPV L ++WPS  E+ A   
Sbjct: 559 VHPLVKTNWLASPPLVVAYALAGTVRIDISSEPLGNDRDGKPVYLRDVWPSSQEV-ATAV 617

Query: 575 ASVKPEQFRKVYEPMFDLSVDYGDKVSP---LYDWRPQSTYIRRPPYW---EGALAGERT 628
           A V    F K Y  +F     +     P    Y W+  STYI+ PP++   +G     + 
Sbjct: 618 AQVNTSMFHKEYAAVFAGDEQWQAIEVPQAATYVWQDDSTYIQHPPFFDAIDGPPPAVKN 677

Query: 629 LKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQR 688
           ++G R LA+LGD++TTDH+SP+  I  DS AG YL + G+   DFNSY + RG+H    R
Sbjct: 678 VEGARILALLGDSVTTDHISPAGNIKADSPAGRYLREQGVEPRDFNSYGSRRGNHQVMMR 737

Query: 689 ATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQ 748
            TFAN +++NEM  +DG  ++G      P G    +++A   Y     PL++IAG +YG 
Sbjct: 738 GTFANIRIRNEM--LDG--EEGGNTIYIPSGERMPIYDAAMLYQAVGTPLVVIAGQEYGT 793

Query: 749 GSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFD 808
           GSSRDWAAKG  L GV+A++AE FERIHR+NLVGMGVLPL+FK  +NR +  + G E  D
Sbjct: 794 GSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFKLDQNRKSLNLTGKETLD 853

Query: 809 VIG----SIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVL 854
           ++G     + PR +L ++ITR++G +  + V CR+DT  EV  ++AGG+L
Sbjct: 854 ILGLNDVELTPRMNLPLVITREDGSQERIEVLCRIDTLNEVEYFKAGGIL 903


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: 2043
Number of extensions: 103
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: 1
Length of query: 867
Length of database: 913
Length adjustment: 43
Effective length of query: 824
Effective length of database: 870
Effective search space:   716880
Effective search space used:   716880
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