Alignments for a candidate for acnD in Mariniradius saccharolyticus AK6

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Mariniradius saccharolyticus AK6

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_008623754.1 C943_RS02195 aconitate hydratase

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000330725.2:WP_008623754.1
          Length = 753

 Score =  217 bits (553), Expect = 2e-60
 Identities = 227/788 (28%), Positives = 347/788 (44%), Gaps = 113/788 (14%)

Query: 78  PARVVCHDILGQTALVDL--AGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDK 135
           P RV   D   Q AL+    AG RD +A            VP+ +  DH +  E G    
Sbjct: 61  PDRVAMQDATAQMALLQFMQAG-RDKVA------------VPSTVHCDHLIQAEIGADAD 107

Query: 136 DAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARNGVA 195
              AK++      N + + F+      +  I     G GI+HQ+ LE            A
Sbjct: 108 LQKAKDK------NREVYDFLASVSNKY-GIGFWKPGAGIIHQVVLENY----------A 150

Query: 196 FPD-TLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGI 254
           FP   ++GTDSHTP+   LG+IAIGVGG +A  VM G    ++ P +IGV LTG+     
Sbjct: 151 FPGGMMIGTDSHTPNAGGLGMIAIGVGGADACDVMAGLPWELKFPKLIGVRLTGRLSGWT 210

Query: 255 TATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQ 314
           +A D++L +   L  +    + +E+FGEGA +L+   + TI NM  E GAT ++F  D++
Sbjct: 211 SAKDVILKVAGILTVKGGTGAVVEYFGEGARSLSATGKGTICNMGAEIGATTSIFGYDEK 270

Query: 315 TLDYLTLTGRE--AEQVKLV-ETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPSN 371
           +  YL  T R   AE    + E     A ++++  K   + + +  +LS +   I GP  
Sbjct: 271 SEAYLRGTDRAEIAEMANSIKEHLTGDAEVYANPEK--YFDQVIDINLSELEPHINGPFT 328

Query: 372 PHARVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANA 431
           P    P S+ A      +   E G      + +  I SCTN+S   ++  A  LA+ A  
Sbjct: 329 PDLAWPLSKFA------QAVKENGW--PAKLEVGLIGSCTNSSY-EDISRAASLAQQAVD 379

Query: 432 KGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQ 491
           K L  K   + ++ PGS+ V+  +E    L   E +G  ++  AC  C G         Q
Sbjct: 380 KKLIAKS--EYTITPGSEQVRFTVERDGFLGVFEKMGGVVLANACGPCIGQWARHGAEKQ 437

Query: 492 QEVIDRDLYATAVLSGNRNFDGRIHPYAK-QAFLASPPLVVAYAIAGTIRFDIEKDVLGL 550
           ++        + + S NRNF  R        AF+ASP +V A AI+G + F+   D L +
Sbjct: 438 EK-------NSIITSFNRNFAKRADGNPNTHAFVASPEIVTAMAISGDLTFNPVTDTL-I 489

Query: 551 DKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPLYDWRPQS 610
           +++GK V+L    P   E+         P +   V +  +      G KV  + D +   
Sbjct: 490 NEEGKAVKLDE--PKGLEL---------PTKGFAVEDAGYQAPASDGSKVQVIVDPKSDR 538

Query: 611 TYIRRP-PYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLP 669
             +  P P WEG       LKG++ L       TTDH+         S AG +L   G  
Sbjct: 539 LQLLAPFPAWEGT-----DLKGLKLLIKAKGKCTTDHI---------SMAGPWLRFRGHL 584

Query: 670 EEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIE 729
           +   N+      +    +       K+KN++    G+V             V R ++A  
Sbjct: 585 DNISNNMLIGAVNAYNGE-----TNKVKNQLGGGYGEVP-----------AVQRQYKA-- 626

Query: 730 TYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLE 789
                    I++   +YG+GSSR+ AA   R  GV AI+ + F RIH TNL   G+L L 
Sbjct: 627 ----HGIGSIVVGDENYGEGSSREHAAMEPRFLGVRAILVKSFARIHETNLKKQGMLALT 682

Query: 790 FKAGENRATYG-IDGTEVFDVIG--SIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVS 846
           F    N A Y  I   +  D++G    AP   LTV++   +G + E+ V    +   ++ 
Sbjct: 683 F---ANPADYDLIQEDDSIDILGLTDFAPGKPLTVVLHHADGSKNEIKVNHTYNEG-QIG 738

Query: 847 IYEAGGVL 854
            + AG  L
Sbjct: 739 WFRAGSAL 746


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: 1488
Number of extensions: 88
Number of successful extensions: 5
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: 753
Length adjustment: 41
Effective length of query: 826
Effective length of database: 712
Effective search space:   588112
Effective search space used:   588112
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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Protein sequences (fasta format)
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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:

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