Alignments for a candidate for acn in Desulfacinum infernum DSM 9756

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Desulfacinum infernum DSM 9756

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_073036524.1 BUB04_RS02125 aconitate hydratase AcnA

Query= SwissProt::Q5SMF6
         (902 letters)



>NCBI__GCF_900129305.1:WP_073036524.1
          Length = 881

 Score =  994 bits (2571), Expect = 0.0
 Identities = 514/881 (58%), Positives = 641/881 (72%), Gaps = 22/881 (2%)

Query: 17  TYGYYDLQELERKGVAEVSRLPFSIRVMLESLLRNEDGYQVTREDIEALARWRPDPGE-I 75
           T+ + DL+ L       + RLP+SIRV+LE+++R  D   VT  D+E LA WR    E +
Sbjct: 13  TFEFVDLKGLFGN---RLGRLPYSIRVLLENVVRRRDDRLVTERDVENLAGWRGRYAEPV 69

Query: 76  NVPLKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPVVPADLVIDHSVQVDAFG 135
            +P   ARV++QDFTGVPAV DLAAMRDA+ A G DP  +NP+VP DLV+DHSVQVD FG
Sbjct: 70  EIPFFPARVLMQDFTGVPAVADLAAMRDALVALGKDPAAVNPLVPVDLVVDHSVQVDFFG 129

Query: 136 TAYAFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIVHQVNIEYLTKVVMTGKR 195
           T+ A   NV +EYERN ERY  LKWAQ + ENFRVVPP +GI HQVN+E+L++V    K 
Sbjct: 130 TSDALTANVRREYERNGERYTFLKWAQKSFENFRVVPPNSGICHQVNLEHLSRVFWDRKE 189

Query: 196 DGLTLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQPYYMLAPRVVGFKLYGE 255
           DG+ + FPD++VG DSHTTMVNG+GVLGWGVGGIEAEAV++GQPY M  P V+G +L G 
Sbjct: 190 DGVRICFPDTVVGLDSHTTMVNGIGVLGWGVGGIEAEAVLMGQPYSMAIPEVIGVRLVGR 249

Query: 256 LPEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDRATIANMAPEYGATMGFF 315
           LP  A ATDLVL VTE LR +GVV KFVEF+GP V  LS P RATIANM+PEYGAT+GFF
Sbjct: 250 LPRRANATDLVLRVTEALRDYGVVEKFVEFFGPAVTALSVPARATIANMSPEYGATVGFF 309

Query: 316 PVDEETLNYLRQTGRPEELVELVEAYTKAVGLFRTPEAEEKVQYSEYLELDLSAVEPSLA 375
           PVDE+ + YLR T R E    + EA  +A+GL+   +  E+  Y++ LE+DLSA+ P++A
Sbjct: 310 PVDEKVVEYLRLTHR-ERQARVTEAAARAMGLYY--DGSEEPDYTDVLEIDLSAIRPAVA 366

Query: 376 GPKRPQDRVPLKEVKKSFLAHLTKPVKERGFGLSEDQLQRKVLVKRRDEEFELTHGSVVI 435
           GP +P+DR+ L E+K  F        + RG    ED  +  V V+ R E  EL+ GSVVI
Sbjct: 367 GPSKPKDRIELSELKTRFR-------QLRG----EDAPKAAVPVRIRGENVELSDGSVVI 415

Query: 436 AAITSCTNTSNPSVMLGAGLLAKKAVEAGLDRKPWVKTSLAPGSKVVTDYLEMSGLMPFL 495
           AAITSCTNTSNP  +LGA LLA+ AV+ GL     VKTSLAPGSKVV  YL+ SGL+P+L
Sbjct: 416 AAITSCTNTSNPHALLGAALLARNAVKRGLAVPAHVKTSLAPGSKVVVQYLDRSGLLPYL 475

Query: 496 EALGFHLVGYGCTTCIGNSGPLPEDIAKAVEEGNLVVAAVLSGNRNFEGRINPHVKANYL 555
           EALGFH V +GCTTCIGNSGPL  ++ +A+EE NL VAAVLSGNRNFE RI+  VK+N+L
Sbjct: 476 EALGFHPVAFGCTTCIGNSGPLHPEVERAIEEHNLNVAAVLSGNRNFEARIHQKVKSNFL 535

Query: 556 ASPMLVVAYALAGRMDIDFTTEPLGFDPNGKPIYLKDIWPSMEEIREAIRKTLDPELFKK 615
           ASP+LVVA+ALAGR+D+D   EP+G DPNG P++L DI P  EEI E + + +  +LF++
Sbjct: 536 ASPLLVVAFALAGRVDVDLEKEPVGLDPNGGPVFLADILPDDEEIEELVNRYVQEDLFRE 595

Query: 616 EYSKVFEGDERWQALPAPTGELYQWDPESTYIQNPPFFEDLGERKVE--DIRGARVLLVL 673
            Y K+ EGD+ W  L       Y WDP STYI+ PP+FE    +  E  DIRGARVLL L
Sbjct: 596 TYEKILEGDQFWNELQVQESVTYPWDPRSTYIKCPPYFEGFTPQMPETTDIRGARVLLWL 655

Query: 674 GDSVTTDHISPAGAIPVKSPAGQYLISKGVKPEDFNSYGSRRGNHEVMMRGTFANIRIKN 733
           GD+VTTDHISPAGAI    PAG+YL S G+  ++FNSYG+RRGNHEVMMRGTFANIRI+N
Sbjct: 656 GDAVTTDHISPAGAIHEDYPAGRYLKSLGLSRQEFNSYGARRGNHEVMMRGTFANIRIRN 715

Query: 734 LMLDGIEGGYAKKLPEGDVDFVYNVAMRYKAEGTPLLVIAGKEYGTGSSRDWAAKGTYLL 793
            ++    G +  K PEG+  +V+  A  Y+ EG PL+V+ GKEYGTGSSRDWAAKG  LL
Sbjct: 716 KLVSE-PGSFTVKFPEGERMYVFEAAEAYRREGVPLIVLGGKEYGTGSSRDWAAKGPKLL 774

Query: 794 GIRAVLAESFERIHRSNLVGMGVLPLEFLPGENRETLGLTGYEVYDILGLEDLKPRKLVD 853
           G++AV+AESFERIHRSNL+GMG+LPL+FL GE+ E+LGL G E Y I G+  ++PR+ + 
Sbjct: 775 GVKAVIAESFERIHRSNLIGMGILPLQFLEGESAESLGLDGTEEYHIAGIAGIEPRRKLT 834

Query: 854 IVARREDGSEVRFQAIARLDTPVEVDYYKNGGILQTVLLNM 894
           + A + DG E  FQ +ARLDT +E DYY+NGGIL  VL  M
Sbjct: 835 VTAVK-DGKEKTFQVLARLDTEIEADYYRNGGILDYVLRKM 874


Lambda     K      H
   0.317    0.137    0.399 

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: 2161
Number of extensions: 87
Number of successful extensions: 7
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: 902
Length of database: 881
Length adjustment: 43
Effective length of query: 859
Effective length of database: 838
Effective search space:   719842
Effective search space used:   719842
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 Apr 09 2024. 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 2024 update 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