Alignments for a candidate for acn in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Dyella japonica UNC79MFTsu3.2

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate N515DRAFT_1420 N515DRAFT_1420 aconitase

Query= BRENDA::P36683
         (865 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1420
          Length = 863

 Score = 1260 bits (3261), Expect = 0.0
 Identities = 627/864 (72%), Positives = 734/864 (84%), Gaps = 8/864 (0%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           ML  YR+HVAERAA GI   PL A Q A L+ELLKNPPAGEE FL+DL++NRVP GVD+A
Sbjct: 1   MLNAYRQHVAERAALGIPALPLTAQQTADLIELLKNPPAGEEAFLVDLISNRVPAGVDDA 60

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           A VKA +LAA+A G+   PLL+  KA ELLGTM GGYNIHPLI+ LDDA++  IAA AL 
Sbjct: 61  AKVKASYLAAVAFGKEPCPLLSRAKATELLGTMLGGYNIHPLIELLDDAQVGGIAADALK 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
            TLLMFD+F+DV+EKA  GN  AK V+QSWADAEWF +RP +   LT+TVFKV GETNTD
Sbjct: 121 KTLLMFDSFHDVKEKADKGNANAKAVLQSWADAEWFTSRPEVPASLTITVFKVPGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREG--IEPDQPGVVGPIKQIEALQQKGFPLAYVGD 238
           DLSPAPDA +RPDIPLHALAMLKN REG   +P++ G  GPI+QI+ L ++G  +AYVGD
Sbjct: 181 DLSPAPDATTRPDIPLHALAMLKNKREGAPFQPEEDGKRGPIQQIQDLARQGHLVAYVGD 240

Query: 239 VVGTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDV 298
           VVGTGSSRKSATNSVLW+ G+DIP +PNKR GG+CLG KIAPIF+NTMEDAGALPIE+DV
Sbjct: 241 VVGTGSSRKSATNSVLWWTGEDIPFIPNKRFGGVCLGSKIAPIFYNTMEDAGALPIELDV 300

Query: 299 SNLNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAR 358
           S ++MGDV+++ PY+G+   +  GE++A F++K+DVL DEVRAGGRIPLIIGRGLT KAR
Sbjct: 301 SQMDMGDVVELRPYEGKALKN--GEVIAEFQVKSDVLFDEVRAGGRIPLIIGRGLTAKAR 358

Query: 359 EALGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQD 415
           EALGL  S +FR  ++ A++ +G++LAQKMVGRACG+   +G+RPG YCEPKMTSVGSQD
Sbjct: 359 EALGLAPSTLFRLPQNPADTGKGYTLAQKMVGRACGLAEGEGVRPGTYCEPKMTSVGSQD 418

Query: 416 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPG 475
           TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDV THH LP FI  RGG+SLRPG
Sbjct: 419 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVKTHHELPAFISTRGGISLRPG 478

Query: 476 DGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR 535
           DGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR
Sbjct: 479 DGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR 538

Query: 536 FKGKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFEL 595
           FKG++QPG+TLRDLV+AIPLYAIKQGLLTV K+GK+NIFSGRILEIEGLP+LKVEQAFEL
Sbjct: 539 FKGELQPGVTLRDLVNAIPLYAIKQGLLTVAKQGKQNIFSGRILEIEGLPNLKVEQAFEL 598

Query: 596 TDASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANP 655
           +DASAERSAAGCT++L++ PIIEYLNSNI LLK+MIA+GY D R+L RRI+ ME+WLANP
Sbjct: 599 SDASAERSAAGCTVRLDQAPIIEYLNSNITLLKYMIAQGYQDARSLSRRIKKMEEWLANP 658

Query: 656 ELLEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIG 715
           +LLE DADAEYAAVI+IDLAD+ EPI+  PNDPDD + LS V G KIDEVFIGSCMTNIG
Sbjct: 659 QLLEPDADAEYAAVIEIDLADVHEPIVACPNDPDDVKSLSDVAGAKIDEVFIGSCMTNIG 718

Query: 716 HFRAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGN 775
           HFRAA KLL+  K  +PTRLWVAPPT+MD  QLTEEG+Y V G +GAR+E+PGCSLCMGN
Sbjct: 719 HFRAASKLLEG-KRDIPTRLWVAPPTKMDQQQLTEEGHYGVLGTAGARMEMPGCSLCMGN 777

Query: 776 QARVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDK 835
           QA+V +GATV+STSTRNFPNRLG   NV+L SAELAA+ + +G++PT EEY   +  ++ 
Sbjct: 778 QAQVREGATVMSTSTRNFPNRLGKNTNVYLGSAELAAICSRLGRIPTKEEYMADIGVINA 837

Query: 836 TAVDTYRYLNFNQLSQYTEKADGV 859
                YRY+NF+Q++ + + AD V
Sbjct: 838 NGEKIYRYMNFDQIADFKQVADTV 861


Lambda     K      H
   0.317    0.136    0.400 

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: 2066
Number of extensions: 79
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: 865
Length of database: 863
Length adjustment: 42
Effective length of query: 823
Effective length of database: 821
Effective search space:   675683
Effective search space used:   675683
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 17 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