GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acnD in Herbaspirillum seropedicae SmR1

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate HSERO_RS11425 HSERO_RS11425 aconitate hydratase

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__HerbieS:HSERO_RS11425
          Length = 873

 Score = 1452 bits (3758), Expect = 0.0
 Identities = 724/862 (83%), Positives = 780/862 (90%), Gaps = 1/862 (0%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64
           MNTQYRK LPGT LDYFD R A+EAI PGA+  LPYTSRVLAENLVRRC+P  LT SL+Q
Sbjct: 1   MNTQYRKQLPGTRLDYFDARAAVEAIRPGAWDTLPYTSRVLAENLVRRCDPATLTDSLRQ 60

Query: 65  IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124
           +IE K+ELDFPWFPARVVCHDILGQTALVDLAGLRDAIA  GGDPA+VNPVVP QLIVDH
Sbjct: 61  LIERKRELDFPWFPARVVCHDILGQTALVDLAGLRDAIADMGGDPAKVNPVVPVQLIVDH 120

Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184
           SLAVE GG D  AF KNRAIEDRRNEDRFHFI+WT+ AF+N+DVIP GNGIMHQINLE+M
Sbjct: 121 SLAVECGGDDPQAFVKNRAIEDRRNEDRFHFIDWTKLAFENVDVIPPGNGIMHQINLEKM 180

Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244
           SPVIHA++GVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAE+VMLGRAS+MRLPDIIGV
Sbjct: 181 SPVIHAKDGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIIGV 240

Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304
           ELTG+ QPGITATDIVL+LTEFLR QKVV +YLEF+G+GA +LTLGDRATISNM PE+GA
Sbjct: 241 ELTGRRQPGITATDIVLSLTEFLRKQKVVGAYLEFYGDGAASLTLGDRATISNMAPEYGA 300

Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364
           TAAMF IDQQT+DYL LTGRE EQVKLVETYAK AGLWSD L +  Y R L FDLS+VVR
Sbjct: 301 TAAMFSIDQQTIDYLKLTGREDEQVKLVETYAKEAGLWSDTLAKVEYERVLRFDLSTVVR 360

Query: 365 TIAGPSNPHARVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGL 424
           T+AGPSNPH R+P SELAA+GI+G+VENEPG MPDGAVIIAAITSCTNTSNPRNVIAAGL
Sbjct: 361 TLAGPSNPHKRLPVSELAAQGIAGKVENEPGKMPDGAVIIAAITSCTNTSNPRNVIAAGL 420

Query: 425 LARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSG 484
           LARNAN  GL RKPWVK+SLAPGSKAV+LYLEEA L  +LE LGFGIV FACTTCNGMSG
Sbjct: 421 LARNANRLGLARKPWVKSSLAPGSKAVELYLEEAGLTADLEKLGFGIVAFACTTCNGMSG 480

Query: 485 ALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 544
           ALDP IQQE+IDRDLY+TAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE
Sbjct: 481 ALDPKIQQEIIDRDLYSTAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 540

Query: 545 KDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPLY 604
           +DVLG+  +G+ +RL +IWPSD EIDAV+ A+VKP+QFR VY PMF   VD    VSPLY
Sbjct: 541 QDVLGVTAEGREIRLKDIWPSDEEIDAVVTAAVKPQQFRNVYTPMFAARVDRSQSVSPLY 600

Query: 605 DWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLH 664
           DWRPQSTYIRRPPYWEGALAGERTL GMRPLAVLGDNITTDHLSPSNAI++DSAAGEYL 
Sbjct: 601 DWRPQSTYIRRPPYWEGALAGERTLSGMRPLAVLGDNITTDHLSPSNAILLDSAAGEYLA 660

Query: 665 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMA-IVDGKVKQGSLARIEPEGIVTR 723
           KMGLPEEDFNSYATHRGDHLTAQRATFANPKL NEM    DG V+QGSLAR+EPEG V R
Sbjct: 661 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVKKADGSVQQGSLARLEPEGKVMR 720

Query: 724 MWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGM 783
           MWE IETYM+RKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNL+GM
Sbjct: 721 MWETIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLIGM 780

Query: 784 GVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAE 843
           GVLPLEFKAGENR TY IDGTE +DVIG   PRADLT++I RKNGERVEVPVTCRLDTAE
Sbjct: 781 GVLPLEFKAGENRNTYAIDGTETYDVIGQRRPRADLTLVIHRKNGERVEVPVTCRLDTAE 840

Query: 844 EVSIYEAGGVLQRFAQDFLESN 865
           EVSIYEAGGVLQRFAQDFLE++
Sbjct: 841 EVSIYEAGGVLQRFAQDFLEAS 862


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: 2276
Number of extensions: 108
Number of successful extensions: 2
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: 867
Length of database: 873
Length adjustment: 42
Effective length of query: 825
Effective length of database: 831
Effective search space:   685575
Effective search space used:   685575
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.

Links

Downloads

Related tools

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