GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acnD in Algiphilus aromaticivorans DG1253

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_043771237.1 U743_RS05220 Fe/S-dependent 2-methylisocitrate dehydratase AcnD

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000733765.1:WP_043771237.1
          Length = 865

 Score = 1400 bits (3623), Expect = 0.0
 Identities = 693/860 (80%), Positives = 763/860 (88%), Gaps = 1/860 (0%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64
           MNT+YRKPLPGT LDYFD R A++AI PGAY  LPYTSRVLAENLVRRC+P MLT +LKQ
Sbjct: 1   MNTEYRKPLPGTELDYFDVRAAVDAIQPGAYDGLPYTSRVLAENLVRRCDPAMLTDALKQ 60

Query: 65  IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124
           +IE +++LDFPW+PARVVCHDILGQTALVDLAGLRDAIA +GGDPA+VNPVVPTQLIVDH
Sbjct: 61  LIERRRDLDFPWYPARVVCHDILGQTALVDLAGLRDAIAERGGDPAKVNPVVPTQLIVDH 120

Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184
           SLAVE+ GF++DAF KNRAIEDRRNEDRFHFI+WT++AF+NIDV+P GNGIMHQINLERM
Sbjct: 121 SLAVEHAGFEEDAFEKNRAIEDRRNEDRFHFIDWTKQAFENIDVVPPGNGIMHQINLERM 180

Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244
           SPV+HA +GVA+PDTLVGTDSHTPHVDALGVIA+GVGGLEAESVMLGRASYMRLPDIIGV
Sbjct: 181 SPVVHAVDGVAYPDTLVGTDSHTPHVDALGVIAVGVGGLEAESVMLGRASYMRLPDIIGV 240

Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304
           ELTGKP PG+T+TDIVLALTEFLR +KVVS+YLEFFGEGA AL+LGDRATISNMTPE+GA
Sbjct: 241 ELTGKPAPGMTSTDIVLALTEFLRNEKVVSAYLEFFGEGASALSLGDRATISNMTPEYGA 300

Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364
           TAAMFYID+QT+DYL LTGR  EQV LVE YA+  GLW+DDLK A Y R L FDLSSV R
Sbjct: 301 TAAMFYIDEQTIDYLKLTGRTPEQVDLVERYARHTGLWADDLKTAEYERVLRFDLSSVTR 360

Query: 365 TIAGPSNPHARVPTSELAARGISGEVE-NEPGLMPDGAVIIAAITSCTNTSNPRNVIAAG 423
            +AGPS PHARV T++LA  GISG+VE  E G MPDGAVIIAAITSCTNTSNPRNVIAAG
Sbjct: 361 NLAGPSRPHARVSTADLAKAGISGKVELPEDGSMPDGAVIIAAITSCTNTSNPRNVIAAG 420

Query: 424 LLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMS 483
           LLARNAN +GLTRKPWVK+S APGSKAV+LY+EE  L  EL  LGFGIV FACTTCNGMS
Sbjct: 421 LLARNANQRGLTRKPWVKSSFAPGSKAVKLYMEECGLQDELNRLGFGIVAFACTTCNGMS 480

Query: 484 GALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDI 543
           GALDP IQQE+IDRDLY+ AVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGT RFDI
Sbjct: 481 GALDPKIQQEIIDRDLYSVAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTTRFDI 540

Query: 544 EKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPL 603
           EKDVLG DKDG  V L ++WPSD EIDA +A++VKPE FR VY+PMF   +   DK+SPL
Sbjct: 541 EKDVLGYDKDGNAVTLKDLWPSDEEIDATVASAVKPEHFRSVYDPMFSFKILDDDKISPL 600

Query: 604 YDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYL 663
           YDWR QSTYIRRPPYWEGALA   +LKGMR LAVLGDNITTDHLSPSNAIM DSAAGEYL
Sbjct: 601 YDWRAQSTYIRRPPYWEGALATAPSLKGMRALAVLGDNITTDHLSPSNAIMADSAAGEYL 660

Query: 664 HKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTR 723
            KMGLPEEDFNSYATHRGDHLTAQRAT ANPKL NEMA+VDG+VKQGSL R+EP+G V R
Sbjct: 661 AKMGLPEEDFNSYATHRGDHLTAQRATLANPKLINEMAVVDGEVKQGSLTRLEPDGKVVR 720

Query: 724 MWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGM 783
           MWEAIE Y +RKQ LI+IAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGM
Sbjct: 721 MWEAIEAYQERKQALIVIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGM 780

Query: 784 GVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAE 843
           GV+PL+F+ G  R T GIDG+E FDV+G+ +P A LT+ I R+ GE +EVPV CRLDT E
Sbjct: 781 GVMPLQFQEGTTRKTMGIDGSETFDVVGTPSPGATLTLHIHRREGETLEVPVICRLDTQE 840

Query: 844 EVSIYEAGGVLQRFAQDFLE 863
           E+ IYEAGGVLQRFAQDFLE
Sbjct: 841 ELRIYEAGGVLQRFAQDFLE 860


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: 2201
Number of extensions: 93
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: 865
Length adjustment: 42
Effective length of query: 825
Effective length of database: 823
Effective search space:   678975
Effective search space used:   678975
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 24 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