Alignments for a candidate for acn in Bacteroides oleiciplenus YIT 12058

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Bacteroides oleiciplenus YIT 12058

Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_009130708.1 HMPREF9447_RS15575 aconitate hydratase

Query= SwissProt::P70920
         (906 letters)



>NCBI__GCF_000315485.1:WP_009130708.1
          Length = 747

 Score =  205 bits (521), Expect = 1e-56
 Identities = 224/828 (27%), Positives = 336/828 (40%), Gaps = 142/828 (17%)

Query: 77  EHEIAFRPARVLMQDFTGVPAVVDLAAMRNAMQKLGGDAEKINPLVPVDLVIDHSVIVNF 136
           E  ++FRP RV MQD T   A+         +Q +    E++   VP  +  DH +    
Sbjct: 54  EDYVSFRPDRVAMQDATAQMAL---------LQFMNAGREQV--AVPSTVHCDHLIQAY- 101

Query: 137 FGDNKAFAKNVTEEYKQNQERYEFLKWGQAAFSNFSVVPPGTGICHQVNLEYLSQTVWTK 196
               +   +++    K N+E Y+FL+   + +       PG GI HQV LE         
Sbjct: 102 ----RGAREDIATATKTNEEVYDFLRDVSSRYG-IGFWQPGAGIIHQVVLE--------- 147

Query: 197 KEKMTVGKKTGTFEVAYPDSL-VGTDSHTTMVNGLAVLGWGVGGIEAEACMLGQPLSMLL 255
                          A+P  + VGTDSHT    GL ++  GVGG +A   M G    + +
Sbjct: 148 -------------NYAFPGGMMVGTDSHTPNAGGLGMVAIGVGGADAVDVMTGMEWELKM 194

Query: 256 PNVVGFKLKGAMKEGVTATDLVLTVTQMLRKLGVVGKFVEFFGPGLDHLSVADKATIANM 315
           P ++G  LKG +       D++L +  +L   G     +E+FGPG   LS   KATI NM
Sbjct: 195 PRLIGVHLKGELNGWAAPKDVILKLAGILTVKGGTNAIIEYFGPGTASLSATGKATICNM 254

Query: 316 APEYGATCGFFPVDAAAIDYLKTSGRAAPRVALVQAYAKAQGLFRTAKSADPVFTETLTL 375
             E GAT   FP D     YLK +GR              +       + +  +   + +
Sbjct: 255 GAEVGATTSIFPYDNRIATYLKATGREEVAEMADSVAGDLRADTDILLAPENYYDRVIEI 314

Query: 376 DLADVVPSMAGPKRPEGRIALPSVAEGFSVALANEYKKTEEPAKRFAVEGKKYEIGHGDV 435
           DL+ + P + GP  P+    +   AE     LAN Y              +K E+G    
Sbjct: 315 DLSRLEPYINGPFTPDAATPISEFAE---KVLANGYP-------------RKMEVG---- 354

Query: 436 VIAAITSCTNTSNPSVLIGAGLLARNAAAKGLK-AKPWVKTSLAPGSQVVAAYLADSGLQ 494
               I SCTN+S    L  A  LAR    K LK A P +   + PGS+ + A     G+ 
Sbjct: 355 ---LIGSCTNSSYQD-LSRAVSLARQVEKKHLKVAAPLI---VNPGSERIRATAERDGMI 407

Query: 495 AHLDKVGFNLVGFGCTTCIGNSGPLPEEISKSINDNGIVAAAVLSGNRNFEGRV--SPDV 552
              +KVG  ++   C  CIG       E       N IV     S NRNF  R   +P+ 
Sbjct: 408 ETFEKVGATIMANACGPCIGQ---WKRETDNPTRKNSIVT----SFNRNFAKRADGNPNT 460

Query: 553 QANYLASPPLVVAHALAGSVTKNLAVEPLGEGKDGKPVYLKDIWPTSKEINAFMKKFVTA 612
            A ++ASP L +A  +AG +  N   + L   ++G+ V L +  P  +E+          
Sbjct: 461 YA-FVASPELTMALTIAGDLCFNPLTDAL-VNREGEKVKLSE--PVGEELP--------- 507

Query: 613 SIFKKKYADVFKGDTNWRKIKTVESETYRWNMSSTYVQNPPYFEGMKKEPEPVTDIVEAR 672
               + +A+  +G    R  KT E      +     +Q  P +EG        TD++   
Sbjct: 508 ---PEGFAEGSEGYIPPRSEKT-EITVNPHSQRLQLLQPFPAWEG--------TDLLNMP 555

Query: 673 ILAMFGDKITTDHISPAGSIKLTSPAGKYLSEHQVRPADFNQYGTRRGNHEVMMRGTFAN 732
           +L     K TTDHIS AG                                 +  RG   N
Sbjct: 556 LLIKTQGKCTTDHISMAGP-------------------------------WLRFRGHLEN 584

Query: 733 IRIKNFMLKGADGNIPEGGLTKHWPDGEQM--SIYDAAMKYQQEQVPLVVFAGAEYGNGS 790
             I + ML GA  N   G     W         +   A  Y+ E +  +V A   YG GS
Sbjct: 585 --ISDNMLMGA-VNAFNGETNSVWNRSTNTYGPVSGTAKMYKSEGISSIVVAEENYGEGS 641

Query: 791 SRDWAAKGTRLLGVRAVICQSFERIHRSNLVGMGVLPLTFEEGTSWSSLGLKGDEKVTLR 850
           SR+ AA   R L VR ++ +SF RIH +NL   G+L LTF +   +    ++  + +++ 
Sbjct: 642 SREHAAMEPRFLNVRVILAKSFARIHETNLKKQGMLALTFVDKADYDK--IQEHDLISVI 699

Query: 851 GLVGDLKPRQKLTAEIVSGDGSLQRVSLLCRIDTLDELDYYRNGGILH 898
           GL  +  P +     +   DG+ +        + L ++ ++R G  L+
Sbjct: 700 GLT-EFAPGRNFKVVLHHEDGTKESFEAQHTYNEL-QISWFRAGSALN 745


Lambda     K      H
   0.317    0.134    0.393 

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: 1541
Number of extensions: 80
Number of successful extensions: 7
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: 906
Length of database: 747
Length adjustment: 42
Effective length of query: 864
Effective length of database: 705
Effective search space:   609120
Effective search space used:   609120
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 (21.6 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:

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