Alignments for a candidate for acnD in Psychrobacter arcticus 273-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Psychrobacter arcticus 273-4

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_011280385.1 PSYC_RS05785 Fe/S-dependent 2-methylisocitrate dehydratase AcnD

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000012305.1:WP_011280385.1
          Length = 885

 Score = 1263 bits (3268), Expect = 0.0
 Identities = 631/874 (72%), Positives = 729/874 (83%), Gaps = 12/874 (1%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64
           MN  ++KPLPGT L YFDTREAIE I  GAY KLP+ S+VL ENLVRRC PE LTA+L+Q
Sbjct: 9   MNEPFKKPLPGTDLYYFDTREAIENIEAGAYDKLPFCSKVLCENLVRRCPPEDLTAALEQ 68

Query: 65  IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124
            I  KQ+LDFPW+PARVVCHDILGQTA VDLAGLRDAIA +GGDP++VNP+VPTQLIVDH
Sbjct: 69  HIYGKQDLDFPWYPARVVCHDILGQTAFVDLAGLRDAIAEQGGDPSKVNPIVPTQLIVDH 128

Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184
           SLAVE+ GF+++AF KNRAIE+RRN+DRFHFINW Q AF N++V+P GNGIMHQINLE+M
Sbjct: 129 SLAVEHAGFEENAFEKNRAIEERRNDDRFHFINWCQYAFDNVNVVPPGNGIMHQINLEKM 188

Query: 185 SPVIH-----ARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLP 239
           SPV+      A   VAF DTLVGTDSHTP VDALGVI+IGVGGLEAESVMLG  SYMRLP
Sbjct: 189 SPVVQVVKNKAGEEVAFADTLVGTDSHTPMVDALGVISIGVGGLEAESVMLGNPSYMRLP 248

Query: 240 DIIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMT 299
           D +GV+LTGK Q GIT TD+VLA+TEFLR   VVS+Y+EFFGEGA  L++GDRA+ISNMT
Sbjct: 249 DYVGVKLTGKLQKGITGTDLVLAMTEFLRNAGVVSTYIEFFGEGARQLSVGDRASISNMT 308

Query: 300 PEFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDL 359
           PE+GATAAMFYID+QT+DYL LTGR   Q+KLVE YAK  GLW+D ++ AVY R L FDL
Sbjct: 309 PEYGATAAMFYIDEQTIDYLRLTGRSEAQIKLVEQYAKQTGLWADGMENAVYDRVLEFDL 368

Query: 360 SSVVRTIAGPSNPHARVPTSELAARGISGEVEN---EP--GLMPDGAVIIAAITSCTNTS 414
           S+VVR +AGPS PHARV T++L A+GI+   E+   EP  GLMPDGAVIIAAITSCTNTS
Sbjct: 369 SAVVRNMAGPSRPHARVSTTDLVAKGIAHAPEDKLPEPKDGLMPDGAVIIAAITSCTNTS 428

Query: 415 NPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGF 474
           NPRN++AAGL+ARNANAKGL RKPWVK+SLAPGSK V++YLEEA L+PEL+ +GF +VGF
Sbjct: 429 NPRNMVAAGLVARNANAKGLLRKPWVKSSLAPGSKTVKMYLEEAGLMPELQEIGFDVVGF 488

Query: 475 ACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYA 534
           ACTTCNGMSGALDP I++E+ID DL+ TAVLSGNRNFDGRIHPYAKQAFLASPPLV+AYA
Sbjct: 489 ACTTCNGMSGALDPDIEKEIIDNDLFTTAVLSGNRNFDGRIHPYAKQAFLASPPLVIAYA 548

Query: 535 IAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFD-LS 593
           IAG IRFDIEKD LG D++G  V L +IW  D E+DA++A +VKPEQF  VY PMFD   
Sbjct: 549 IAGNIRFDIEKDSLGKDQNGNDVYLKDIWFDDDEVDAIVAKAVKPEQFNAVYIPMFDEAK 608

Query: 594 VDYGDKVSPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAI 653
            D G  +SPLY+WR Q+TYIRRPPYWEG +A    L GMRPLAVLGDNITTDHLSPSNAI
Sbjct: 609 KDTGKALSPLYNWRDQTTYIRRPPYWEGKMAAMNKLTGMRPLAVLGDNITTDHLSPSNAI 668

Query: 654 MMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVD-GKVKQGSL 712
           + DSAAGEYL  MGLP ED+NSYATHRGDHLTAQRATFANPKL NEM   + G V QGSL
Sbjct: 669 LGDSAAGEYLDTMGLPSEDYNSYATHRGDHLTAQRATFANPKLLNEMVRDEKGDVIQGSL 728

Query: 713 ARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGF 772
           AR+EPEG V RMWEAIETYM+R+QPLIIIAG  YGQGSSRDWAAKGVRLAGVE +VAE F
Sbjct: 729 ARVEPEGQVMRMWEAIETYMNREQPLIIIAGDGYGQGSSRDWAAKGVRLAGVEVVVAEDF 788

Query: 773 ERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVE 832
           ERIHR NLVGMG LPL+F+ G  R T  IDGTEVFDV G ++    + ++I R +G ++E
Sbjct: 789 ERIHRQNLVGMGALPLQFEKGVTRNTLNIDGTEVFDVTGEVSAGGMMALVINRADGSKLE 848

Query: 833 VPVTCRLDTAEEVSIYEAGGVLQRFAQDFLESNL 866
           VP+ CRLDTA+EV +Y AGG+LQRFA++F++  L
Sbjct: 849 VPIICRLDTADEVKMYNAGGMLQRFAKEFIDGTL 882


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: 2172
Number of extensions: 86
Number of successful extensions: 5
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: 885
Length adjustment: 42
Effective length of query: 825
Effective length of database: 843
Effective search space:   695475
Effective search space used:   695475
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources