Alignments for a candidate for acn in Caminibacter mediatlanticus TB-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Caminibacter mediatlanticus TB-2

Align Aconitate hydratase B; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; 2-methyl-cis-aconitate hydratase; Iron-responsive protein-like; IRP-like; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_007474665.1 CMTB2_RS05535 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= SwissProt::Q8ZRS8
         (865 letters)



>NCBI__GCF_000170735.1:WP_007474665.1
          Length = 861

 Score = 1083 bits (2800), Expect = 0.0
 Identities = 547/859 (63%), Positives = 677/859 (78%), Gaps = 24/859 (2%)

Query: 2   LEEYRKHVAERAAQGIVPKPLDATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEAA 61
           +EEY+KH  ERA  GI P PL A Q A LVELLK  P+ EEE+L+DL +N + PGVDEAA
Sbjct: 4   IEEYKKHTEERAKLGIPPLPLTAAQTAELVELLKKVPIVEEEYLMDLFLNHINPGVDEAA 63

Query: 62  YVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLIDAL--DDAKLAPIAAKAL 119
           YVKA FL  + +G  +SP +S ++A+E+LGTM GGYN+ PLIDAL  +D ++A  AA  L
Sbjct: 64  YVKAAFLNDIVQGKASSPAISKKRAVEILGTMLGGYNVKPLIDALSHEDEEVAKEAANQL 123

Query: 120 SHTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITVTVFKVTGETNT 179
            +TLL++D F+DV+E A  GN+YAK+V++SW++AEWF S+ PL EKI   VFKV GETNT
Sbjct: 124 KNTLLVYDAFHDVKELADKGNKYAKEVLESWSEAEWFTSKKPLPEKIEAIVFKVPGETNT 183

Query: 180 DDLSPAPDAWSRPDIPLHAQAMLKNAREGIEPDQPGVVGPIKQIEALQKKGYPLAYVGDV 239
           DDLSPA +A++R DIPLHA +MLK       PD       I++I  L+K G P+A+VGDV
Sbjct: 184 DDLSPASEAFTRSDIPLHALSMLKAKM----PDA------IEKINELKKSGKPVAFVGDV 233

Query: 240 VGTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVS 299
           VGTGSSRKSA NSV+W +G++IP VPNK+ GG+ +GG IAPIFFNT+ED+GALPI+  V 
Sbjct: 234 VGTGSSRKSAANSVIWHIGEEIPYVPNKKRGGIVIGGVIAPIFFNTLEDSGALPIQAPVD 293

Query: 300 NLNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKARE 359
            L  GD+I++YPY+G++  +  GE+++ FEL  + L DEVRAGGR+PLIIG+ LT KARE
Sbjct: 294 KLETGDIIEIYPYEGKIVKN--GEVVSEFELSPNTLPDEVRAGGRVPLIIGKNLTKKARE 351

Query: 360 ALGLPHSDVF-RQAKDVAESSRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTG 418
            LG    ++F R A+   +   G++ AQK++G+ACG++G+RPG Y EP  T+VGSQDTTG
Sbjct: 352 VLGKEEENIFIRPAQPEDKKGVGYTQAQKIIGKACGMEGVRPGMYVEPTATTVGSQDTTG 411

Query: 419 PMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDGV 478
            MTRDE+K+LA LGF+ADLVMQSFCHTAAYPKP D+  HHTLPDFI +RGGV+LRPGDGV
Sbjct: 412 AMTRDEIKELAALGFNADLVMQSFCHTAAYPKPADIKLHHTLPDFITSRGGVALRPGDGV 471

Query: 479 IHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKG 538
           IHSWLNRM+LPDT+GTGGDSHTRFPIGISFPAGSGLVAFAA TG MPL++PESVLVRFKG
Sbjct: 472 IHSWLNRMILPDTLGTGGDSHTRFPIGISFPAGSGLVAFAAVTGSMPLNVPESVLVRFKG 531

Query: 539 KMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEG--LPDLKVEQAFELT 596
           ++QPGITLRDLV+AIP +AIKQGLLTVEKK KKNIF+GRILEIEG  +  L VEQAFEL 
Sbjct: 532 ELQPGITLRDLVNAIPYFAIKQGLLTVEKKNKKNIFNGRILEIEGDIIRTLTVEQAFELA 591

Query: 597 DASAERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADPQ 656
           DASAERSAA CT+ +++E + EYL SNI LL+ MI  GY D+RTL+RRI  M++WL +P+
Sbjct: 592 DASAERSAAACTVDVSEEQVAEYLKSNIKLLEEMIEAGYEDKRTLQRRIDKMKEWLDNPK 651

Query: 657 LLEADADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGE-----KIDEVFIGSCM 711
           LL  D DAEYAAVI+IDL +I EPI+  PNDPDD   +S+V  +     KIDEVF+GSCM
Sbjct: 652 LLRRDEDAEYAAVIEIDLNEITEPIVACPNDPDDVATISEVLADPNRPHKIDEVFLGSCM 711

Query: 712 TNIGHFRAAGKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSL 771
           TNIGH+RAAG++L   +GQ+P RLW+APPT+MD AQL EEGYYS+FG++GARIEIPGCSL
Sbjct: 712 TNIGHYRAAGEILKG-EGQVPVRLWIAPPTKMDKAQLIEEGYYSIFGQAGARIEIPGCSL 770

Query: 772 CMGNQARVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVA 831
           CMGNQARVAD A V STSTRNF NR+G GA V+L SAELAAV AL+G++PT EEY   + 
Sbjct: 771 CMGNQARVADYANVFSTSTRNFDNRMGKGAKVYLGSAELAAVIALLGRIPTKEEYLEIIE 830

Query: 832 QVDKTAVD-TYRYLNFDQL 849
           +      D  Y YLNF ++
Sbjct: 831 KKLAGKEDKVYNYLNFHKM 849


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: 1986
Number of extensions: 84
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: 865
Length of database: 861
Length adjustment: 42
Effective length of query: 823
Effective length of database: 819
Effective search space:   674037
Effective search space used:   674037
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 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