Alignments for a candidate for acnD in Allochromatium vinosum DSM 180

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Allochromatium vinosum DSM 180

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_012970720.1 ALVIN_RS07480 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000025485.1:WP_012970720.1
          Length = 887

 Score =  682 bits (1759), Expect = 0.0
 Identities = 371/855 (43%), Positives = 523/855 (61%), Gaps = 40/855 (4%)

Query: 36  AKLPYTSRVLAENLVRRCEPEMLTASLKQII-----ESKQELDFPWFPARVVCHDILGQT 90
           A+LP++ ++L ENL+R  +   +T    +       +++ + +  + PARV+  D  G  
Sbjct: 30  ARLPFSIKILLENLLRNEDGVTVTREDIEYFSNWNPQAEPDKEIQYRPARVLMQDFTGVP 89

Query: 91  ALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNE 150
           A+VDLA +RDA+ A GGDP ++NP+ P +L++DHS+ V++ G D  AFA N  +E +RN+
Sbjct: 90  AVVDLAAMRDAMRALGGDPTRINPLQPAELVIDHSVQVDHFGSD-GAFALNAELEFQRNQ 148

Query: 151 DRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHAR----NGVAFPDTLVGTDSH 206
           +R+ F+ W Q+AF    V+P   GI+HQ+N+E ++ V+  +       A+ DT VGTDSH
Sbjct: 149 ERYKFLKWGQQAFDGFKVVPPDTGIVHQVNVEYLARVVFPKPVDGTTQAYFDTCVGTDSH 208

Query: 207 TPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALTEF 266
           T  V+ +GV+  GVGG+EAE+ MLG+   M +P ++G +LTG  + G+TATD+VL + E 
Sbjct: 209 TTMVNGIGVLGWGVGGIEAEASMLGQPVSMLVPKVVGFKLTGTLKEGVTATDLVLTIVEQ 268

Query: 267 LRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGREA 326
           LR   VV  ++EF+G    +L +G+R TI+NM PE+GAT  +F IDQ TLDYL LTGR+ 
Sbjct: 269 LRKHGVVGKFVEFYGPAIASLPMGERNTIANMGPEYGATCGLFPIDQVTLDYLRLTGRDE 328

Query: 327 EQVKLVETYAKTAGLW-SDDLKQAVYPRTLHFDLSSVVRTIAGPSNPHARVPTSELAAR- 384
            Q+ LVE Y K  G+W + D  +A Y  TL  DL  V  ++AGP  P  RV  +++A+  
Sbjct: 329 AQIALVEAYCKAQGVWHTADAPEAEYSETLELDLGDVAPSLAGPKRPQDRVALTDMASHF 388

Query: 385 -----------------GISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGLLAR 427
                                 ++ +   + DG++++AAITSCTNTSNP  +I AGL+A+
Sbjct: 389 PKALAALKAERNLPTKGAAKAVIDGQEVEISDGSIVVAAITSCTNTSNPSVLIGAGLVAK 448

Query: 428 NANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALD 487
            A A GL R PWVKT+  PGS AV  YL+ A L   L++LGF  VG+ CT C G +G L 
Sbjct: 449 KAVALGLKRAPWVKTAFGPGSMAVTRYLDRAGLTEPLKALGFHNVGYGCTVCIGNTGPLP 508

Query: 488 PVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDV 547
             + + + D +L A ++LSGNRNF+GR+H   +  +LASPPLVVAYAIAG I  D   D 
Sbjct: 509 EPVSKAIADNELCAVSILSGNRNFEGRVHAEVRMNYLASPPLVVAYAIAGRIDIDPYNDP 568

Query: 548 LGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMF--DLSVDYGDKV-SPLY 604
           L  D  G PV L +IWP+  E++A IA  V P +F   Y  +F  D      D V +  Y
Sbjct: 569 LTTDAQGNPVYLKDIWPTQDEVNAAIAEFVTPAEFTAAYADVFAGDARWQSLDAVATQTY 628

Query: 605 DWRPQSTYIRRPPYWEG---ALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGE 661
           DW   STYIR PPY++G    +A    +   R LAVLGD+ITTDH+SP+ +I  +S AG+
Sbjct: 629 DWPADSTYIRNPPYFQGMSLEVAPVEDISRARCLAVLGDSITTDHISPAGSIKPNSPAGK 688

Query: 662 YLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIV 721
           YL + G+  +DFNS  + RG+H    R TFAN +L+N MA       +G +   +P    
Sbjct: 689 YLIEHGVEPKDFNSLGSRRGNHEVMMRGTFANIRLRNLMA----PGTEGGVTLHQPSQEQ 744

Query: 722 TRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLV 781
             +++A   Y     P I+IAG +YG GSSRDWAAKG RL G+ A++AE +ERIHR+NLV
Sbjct: 745 LSIYDAAMRYQAEGTPAIVIAGKEYGSGSSRDWAAKGPRLLGIRAVIAESYERIHRSNLV 804

Query: 782 GMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRA-DLTVIITRKNGERVEVPVTCRLD 840
           GMG+LPL+F AGEN A+ G+ GTE FD++G     A  + V  T  +G         R+D
Sbjct: 805 GMGILPLQFLAGENAASLGLIGTETFDIVGLNGGEAKQVEVRATGADGSVKTFQARVRID 864

Query: 841 TAEEVSIYEAGGVLQ 855
           T  EV  Y  GG+LQ
Sbjct: 865 TPNEVDYYRHGGILQ 879


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: 1944
Number of extensions: 103
Number of successful extensions: 10
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: 887
Length adjustment: 42
Effective length of query: 825
Effective length of database: 845
Effective search space:   697125
Effective search space used:   697125
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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