Aligments for a candidate for acn in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Aligments for a candidate for acn in Sphingomonas koreensis DSMZ 15582

Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; IP210; Iron-responsive protein-like; IRP-like; Major iron-containing protein; MICP; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate Ga0059261_3296 Ga0059261_3296 aconitate hydratase 1

Query= SwissProt::P37032
         (891 letters)



>FitnessBrowser__Korea:Ga0059261_3296
          Length = 890

 Score = 1149 bits (2972), Expect = 0.0
 Identities = 585/891 (65%), Positives = 688/891 (77%), Gaps = 8/891 (0%)

Query: 3   VGQDSLSTKSQLTVDGKTYNYYSLKEAENKHFKGINRLPYSLKVLLENLLRFEDGNTVTT 62
           +GQDSL T+  LTV GK+Y+YYSL++A  K    ++RLP+S+KVLLEN+LRFEDG TVT 
Sbjct: 4   IGQDSLGTRETLTVGGKSYSYYSLEKAAAK-LGDVSRLPFSMKVLLENMLRFEDGVTVTP 62

Query: 63  KDIKAIADWLHNKTS-QHEIAFRPTRVLMQDFTGVPAVVDLAAMRTAIVKMGGNADKISP 121
           +D +AI DW  N  + + EI +RP RVLMQDFTGVP VVDLAAMR AI K+GG+A KI+P
Sbjct: 63  EDAQAIVDWQKNPNAPEREIQYRPARVLMQDFTGVPCVVDLAAMRDAITKLGGDAAKINP 122

Query: 122 LSPVDLVIDHSVMVDKFASADALEVNTKIEIERNKERYEFLRWGQKAFSNFQVVPPGTGI 181
             PV LVIDHSVMVD+F +  A E N ++E +RN ERY+FL+WG K+  NF+VVPPGTGI
Sbjct: 123 QVPVHLVIDHSVMVDEFGTPKAFEENVELEYQRNMERYDFLKWGSKSLDNFKVVPPGTGI 182

Query: 182 CHQVNLEYLGKTVWNSEN-DGQLYAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAML 240
           CHQVNLEY+   +W+S   DG   AYPDTLVGTDSHTTM+NGLGVLGWGVGGIEAEAAML
Sbjct: 183 CHQVNLEYIADAIWSSTAADGTTVAYPDTLVGTDSHTTMVNGLGVLGWGVGGIEAEAAML 242

Query: 241 GQPVSMLIPEVIGFKLSGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGPGLNDLPLA 300
           GQPVSMLIPEV+GFKL+GKL+EGITATDLVLTVTQMLR +GVVG+FVEF+GPGL  + LA
Sbjct: 243 GQPVSMLIPEVVGFKLTGKLQEGITATDLVLTVTQMLRARGVVGRFVEFFGPGLATMTLA 302

Query: 301 DRATISNMAPEYGATCGFFPVDKETIKYLELTGRDKHTIALVEAYAKAQGMWYDKDNEEP 360
           DRATI+NMAPEYGATCGFF +D +T+ Y+ LTGRD  T+ LVEAY KAQGMW   D  +P
Sbjct: 303 DRATIANMAPEYGATCGFFGIDDKTLDYMRLTGRDDDTVTLVEAYCKAQGMWRYDDMADP 362

Query: 361 VFTDSLHLDLGSVEPSLAGPKRPQDKVNLSSLPVEFNNFLIEVGKEKEKEKTFAVKNKDF 420
           +FTD+L LD+ +V  SLAGPKRPQD+V+L+ +   FN  L +V   KE     AV+ KD 
Sbjct: 363 IFTDTLELDMATVTASLAGPKRPQDRVSLNKVDEVFNGDLFKV-YGKENGHRVAVEGKDH 421

Query: 421 QMKHGHVVIAAITSCTNTSNPSVLMAAGLVAKKAIEKGLQRKPWVKSSLAPGSKVVTDYL 480
            +  G VVIAAITSCTNTSNPSVL+AAGLVA+KA  KGL RKPWVK+SLAPGS+VVTDYL
Sbjct: 422 DIGDGDVVIAAITSCTNTSNPSVLIAAGLVARKARAKGLTRKPWVKTSLAPGSQVVTDYL 481

Query: 481 RHAGLQTYLDQLGFNLVGYGCTTCIGNSGPLPDDISHCVAEHDLVVSSVLSGNRNFEGRV 540
             AGL   LD +GFNLVGYGCTTCIGNSGPL   IS  +  +D+V +SVLSGNRNFEGRV
Sbjct: 482 NKAGLSEDLDAIGFNLVGYGCTTCIGNSGPLAQPISDAINGNDIVAASVLSGNRNFEGRV 541

Query: 541 HPQVRANWLASPPLVVAYALCGTTCSDLSREPIGQDKEGNDVYLKDIWPSNEEIAAEV-A 599
            P VRAN+LASPPLVVAYAL GT   D+   PIG+  +G  VYLKDIWP+NEE+   + A
Sbjct: 542 SPDVRANFLASPPLVVAYALKGTVTEDMIETPIGEGTDG-PVYLKDIWPTNEEVQGVINA 600

Query: 600 KVSGTMFRKEYAEVFKGDAHWQAIQTSSGQTYEWNPDSTYIQHPPFFENLSLKPEPLKPI 659
            +   MF+  Y  V+ GDAHWQ I      TY W   STYI +PP+F  +++ P P+  I
Sbjct: 601 NIDSEMFKSRYGNVYLGDAHWQKINVEGSATYSWPAASTYIANPPYFAGMTMTPAPVADI 660

Query: 660 KQAYVLALFGDSITTDHISPAGSIKASSPAGLYLKSKGVDEKDFNSYGSRRGNHEVMMRG 719
             A  LA+ GDSITTDHISPAGSIKA SPAG +L  + V + DFNSYG+RRGN  VM+RG
Sbjct: 661 VDAKPLAILGDSITTDHISPAGSIKADSPAGKWLMERQVSKADFNSYGARRGNDNVMVRG 720

Query: 720 TFANIRIRNEMTPGQEGGVTRYVPTGETMSIYDAAMRYQENQQDLVIIAGKEYGTGSSRD 779
           TFANIRIRNEM PG EGG+T Y   GETM IYDAAMR++ +   LVI+AGKEYGTGSSRD
Sbjct: 721 TFANIRIRNEMVPGVEGGMTSY--AGETMPIYDAAMRHKADGTPLVIVAGKEYGTGSSRD 778

Query: 780 WAAKGTNLLGVKAVITESFERIHRSNLIGMGILPLQFKEGTTRKTLKLDGSERISIEISD 839
           WAAKGTNLLGV+AVITESFERIHRSNL+GMG+LPLQF EG TR+TLKLDGSE  +I    
Sbjct: 779 WAAKGTNLLGVRAVITESFERIHRSNLVGMGVLPLQFAEGVTRQTLKLDGSETFTITGVA 838

Query: 840 KLTPGAMVPVTIERQDGDIEKIETLCRIDTADELEYYKNGGILQYVLRKIS 890
            L P   V V + R DG  E   T CRIDT +ELEY+ NGGILQYVLR ++
Sbjct: 839 GLRPRQDVEVKLTRADGSSETFLTRCRIDTVNELEYFLNGGILQYVLRNLA 889


Lambda     K      H
   0.316    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: 2101
Number of extensions: 88
Number of successful extensions: 8
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: 891
Length of database: 890
Length adjustment: 43
Effective length of query: 848
Effective length of database: 847
Effective search space:   718256
Effective search space used:   718256
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 17 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, or view the source code.

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