Alignments for a candidate for acn in Geobacter metallireducens GS-15

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Geobacter metallireducens GS-15

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_004513187.1 GMET_RS05080 aconitate hydratase AcnA

Query= SwissProt::Q5SMF6
         (902 letters)



>NCBI__GCF_000012925.1:WP_004513187.1
          Length = 937

 Score = 1080 bits (2792), Expect = 0.0
 Identities = 553/930 (59%), Positives = 680/930 (73%), Gaps = 39/930 (4%)

Query: 3   NSFQTLKTLTTKSGTYGYYDLQELERKGVAEVSRLPFSIRVMLESLLRNEDGYQVTREDI 62
           +SF++   L      Y Y+ L +      A++SRLP+SI+++LE+LLR EDG  V R+DI
Sbjct: 7   DSFESRAILAVGQSRYHYHSLPKFAESFRADISRLPYSIKILLENLLRREDGVTVERDDI 66

Query: 63  EALARWRPDP-GEINVPLKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPVVPA 121
            AL  W P    +  +    ARV+LQDFTGVPA+ DLAAMR A+K  GGDP RINP+ PA
Sbjct: 67  VALGHWHPRTLPDREIQFMPARVLLQDFTGVPAIADLAAMRAALKRLGGDPARINPLQPA 126

Query: 122 DLVIDHSVQVDAFGTAYAFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIVHQV 181
           DL+IDHSVQVD +GT  A   N + E+ RNRERY  L+W Q A  NFRV+PP TGI HQV
Sbjct: 127 DLIIDHSVQVDRYGTKSAASANADFEFRRNRERYQFLRWGQGAFRNFRVIPPDTGICHQV 186

Query: 182 NIEYLTKVVMTGKRDGLTLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQPYY 241
           N+EYL ++ M  ++DG    +PD+LVGTDSHTTMVNGLGV+GWGVGGIEAEA +LGQP  
Sbjct: 187 NLEYLARIAMVAEQDGENWVYPDTLVGTDSHTTMVNGLGVVGWGVGGIEAEAALLGQPCS 246

Query: 242 MLAPRVVGFKLYGELPEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDRATI 301
           ML PRVVGF+  G LP GATATDLVLTVT+MLRK GVVG FVEF+GPG+A L+  DRATI
Sbjct: 247 MLIPRVVGFRFLGRLPPGATATDLVLTVTQMLRKKGVVGAFVEFFGPGLASLTVADRATI 306

Query: 302 ANMAPEYGATMGFFPVDEETLNYLRQTGRPEELVELVEAYTKAVGLFRTPEAEEKVQYSE 361
            NMAPEYGAT+G FPVD +TL+YLR TGR   LV LVEAY +A G++   +  E   YS+
Sbjct: 307 GNMAPEYGATIGIFPVDGQTLDYLRLTGR-AALVPLVEAYYRAQGMWYDADQPEP-WYSD 364

Query: 362 YLELDLSAVEPSLAGPKRPQDRVPLKEVKKSF-----------LAHLTKPVKERGFG--- 407
            +ELDL  VEP LAGP RPQDR+PLKEV+ SF            A + + + +R FG   
Sbjct: 365 TIELDLGTVEPCLAGPSRPQDRIPLKEVRGSFRKSLAGLMQNETARIDRGILDRWFGDGG 424

Query: 408 --------LSED-------QLQRKVLVKRRD-EEFELTHGSVVIAAITSCTNTSNPSVML 451
                   LS          L+R V V++ D   + L HGS+VIAAITSCTNTSNPSV++
Sbjct: 425 APRYVAPELSISPPDEKLGPLERCVPVRQPDGVAYNLCHGSIVIAAITSCTNTSNPSVLM 484

Query: 452 GAGLLAKKAVEAGLDRKPWVKTSLAPGSKVVTDYLEMSGLMPFLEALGFHLVGYGCTTCI 511
            AGLLA+ AV+ GL  KPWVKTS APGS+VVTDYL  +GL  +LE L FHLVGYGCTTCI
Sbjct: 485 AAGLLARNAVQRGLQVKPWVKTSFAPGSRVVTDYLASAGLTAYLEGLRFHLVGYGCTTCI 544

Query: 512 GNSGPLPEDIAKAVEEGNLVVAAVLSGNRNFEGRINPHVKANYLASPMLVVAYALAGRMD 571
           GNSGPLP+ IA+AV +G L VAAVLSGNRNFEGRIN +V+ NYLASP LVVAYALAG + 
Sbjct: 545 GNSGPLPDHIARAVVDGGLAVAAVLSGNRNFEGRINNYVRTNYLASPPLVVAYALAGNIA 604

Query: 572 IDFTTEPLGFDPNGKPIYLKDIWPSMEEIREAIRKTLDPELFKKEYSKVFEGDERWQALP 631
           +D T +P+G DPNG+P+YLKDIWP+ EE+ + +R+ + PE F + Y+ +  G+  W+ LP
Sbjct: 605 MDLTRDPVGIDPNGQPVYLKDIWPADEEVADLVRRHVTPEHFSRGYADILRGNTAWEGLP 664

Query: 632 APTGELYQWDPESTYIQNPPFFEDLG--ERKVEDIRGARVLLVLGDSVTTDHISPAGAIP 689
            P  ELYQW+  STY++ PPFF D+      V+DIRGARVL +LGDSVTTDHISPAGAI 
Sbjct: 665 VPASELYQWEETSTYLKEPPFFADVTAVPAPVDDIRGARVLALLGDSVTTDHISPAGAIA 724

Query: 690 VKSPAGQYLISKGVKPEDFNSYGSRRGNHEVMMRGTFANIRIKNLMLDGIEGGYAKKLP- 748
            +SPAG+YL+S GVKPEDFNSYGSRRGNHEVM+RGTFAN+RI+NL++ G+EGG     P 
Sbjct: 725 PESPAGRYLVSLGVKPEDFNSYGSRRGNHEVMVRGTFANVRIRNLLVPGVEGGMTNYFPQ 784

Query: 749 ---EGDVDFVYNVAMRYKAEGTPLLVIAGKEYGTGSSRDWAAKGTYLLGIRAVLAESFER 805
              +G+   +Y+ AMRY+ +G PL+V+AG EYGTGSSRDWAAKGT LLG+RAV+A+SFER
Sbjct: 785 GKDQGETMPIYDAAMRYQQDGIPLIVVAGAEYGTGSSRDWAAKGTRLLGVRAVIAQSFER 844

Query: 806 IHRSNLVGMGVLPLEFLPGENRETLGLTGYEVYDILGLEDLKPRKLVDIVARREDGSEVR 865
           IHRSNL+GMGVLPL+F+ GE+RET GLTG E Y+I GL  L P   + + AR   G+   
Sbjct: 845 IHRSNLIGMGVLPLQFMAGESRETHGLTGEETYEIEGLASLIPGGTLRVTARSAGGNGRE 904

Query: 866 FQAIARLDTPVEVDYYKNGGILQTVLLNML 895
           FQ + R+DTP E+DYY++GGIL  VL   L
Sbjct: 905 FQVLVRIDTPNELDYYRHGGILPYVLRQTL 934


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: 2403
Number of extensions: 128
Number of successful extensions: 6
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: 937
Length adjustment: 43
Effective length of query: 859
Effective length of database: 894
Effective search space:   767946
Effective search space used:   767946
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: 57 (26.6 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