Alignments for a candidate for acn in Calditerrivibrio nitroreducens DSM 19672

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Calditerrivibrio nitroreducens DSM 19672

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_013451188.1 CALNI_RS05335 aconitate hydratase AcnA

Query= SwissProt::Q5SMF6
         (902 letters)



>NCBI__GCF_000183405.1:WP_013451188.1
          Length = 877

 Score = 1001 bits (2588), Expect = 0.0
 Identities = 506/881 (57%), Positives = 643/881 (72%), Gaps = 23/881 (2%)

Query: 18  YGYYDLQELERKGVAEVSRLPFSIRVMLESLLRNEDGYQVTREDIEALARW-RPDPGEIN 76
           Y +YD+ +L + G  ++ +LP+SI++++E++LRN    QV  +D++ +A W R  P  I 
Sbjct: 17  YFFYDINKLSKDGF-DIKKLPYSIKILVENILRNLGDGQVNEKDLKNIAGWSRKQPIPIE 75

Query: 77  VPLKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPVVPADLVIDHSVQVDAFGT 136
           +P K  RV++QDFTGVPAVVDLAAMRDA+   G +P++INP+VP DL++DHSVQVD +GT
Sbjct: 76  IPYKPVRVLMQDFTGVPAVVDLAAMRDAMLELGKNPEKINPLVPVDLIVDHSVQVDYYGT 135

Query: 137 AYAFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIVHQVNIEYLTKVVMTGKRD 196
             +   NV  EY+RN ERY LLKWAQ +  NFRVVPP +GI HQVN+EYL KVV    R 
Sbjct: 136 EDSILKNVALEYKRNEERYKLLKWAQKSFHNFRVVPPNSGICHQVNLEYLAKVVCIDDRK 195

Query: 197 GLTLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQPYYMLAPRVVGFKLYGEL 256
              L + D+ +GTDSHT MVNG+GV+GWGVGGIEAEAVMLGQPYYM  P V+G KL GEL
Sbjct: 196 DKKLLYLDTCIGTDSHTPMVNGIGVMGWGVGGIEAEAVMLGQPYYMPIPEVIGVKLIGEL 255

Query: 257 PEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDRATIANMAPEYGATMGFFP 316
            EG TATDL+LT+TE LR++GVV KFVE++GPGV  LS PDRATI+NM PE+GAT+G FP
Sbjct: 256 NEGVTATDLILTITEKLRRYGVVDKFVEYFGPGVKTLSIPDRATISNMTPEFGATLGIFP 315

Query: 317 VDEETLNYLRQTGRPEELVELVEAYTKAVGLFRTPEAEEKVQYSEYLELDLSAVEPSLAG 376
           +D +T+ YLR T R +   +++E Y K  G+F T   +EKV+Y++ LE+DL+++EPS+AG
Sbjct: 316 IDRKTIEYLRMTNR-DRYADILEIYAKKAGIFYT--GQEKVEYTDVLEIDLNSIEPSIAG 372

Query: 377 PKRPQDRVPLKEVKKSFLAHLTKPVKERGFGLSEDQLQRKVLVKRRDEEFELTHGSVVIA 436
           P RPQDR+ L +VK +               L   +    V ++       +  GSVVIA
Sbjct: 373 PSRPQDRISLSQVKSN---------------LQNLKTDNFVDIEIDQNPVRIKDGSVVIA 417

Query: 437 AITSCTNTSNPSVMLGAGLLAKKAVEAGLDRKPWVKTSLAPGSKVVTDYLEMSGLMPFLE 496
           AITSCTNTSNP V++GAGL+A+ AV+ GL  KP+VKTS APGSKVV  YL+ SGLMP+LE
Sbjct: 418 AITSCTNTSNPFVIIGAGLMARNAVKKGLRVKPYVKTSFAPGSKVVESYLKKSGLMPYLE 477

Query: 497 ALGFHLVGYGCTTCIGNSGPLPEDIAKAVEEGNLVVAAVLSGNRNFEGRINPHVKANYLA 556
           ALGFH+  YGCTTCIGNSGP+   I +A+ + NL VAAVLSGNRNFE RI+  V++N+LA
Sbjct: 478 ALGFHITAYGCTTCIGNSGPVLPQIEEAIIKNNLNVAAVLSGNRNFEARIHQLVRSNFLA 537

Query: 557 SPMLVVAYALAGRMDIDFTTEPLGFDPNGKPIYLKDIWPSMEEIREAIRKTLDPELFKKE 616
           SPMLVVAYALAG++DIDF  EPLG+ P G+ + LKD+WPS EEI E I  T     FK++
Sbjct: 538 SPMLVVAYALAGKIDIDFKNEPLGYTPYGEKVMLKDLWPSSEEIHEIISDTFTKSDFKRD 597

Query: 617 YSKVFEGDERWQALPAPTGELYQWDPESTYIQNPPFFEDLGER--KVEDIRGARVLLVLG 674
           Y K+F+GD  WQ +     + Y W  +STYI+ PP+F++  +   K+ DI  AR+LL+LG
Sbjct: 598 YGKIFDGDLFWQKMNVKVDKTYHWHEKSTYIKKPPYFDNFMKEPGKIFDITNARILLLLG 657

Query: 675 DSVTTDHISPAGAIPVKSPAGQYLISKGVKPEDFNSYGSRRGNHEVMMRGTFANIRIKNL 734
           DS+TTDHISPAG I    PAG+YLISKGVK +DFNSYGSRRGNHEVM+RGTF NIRIKN 
Sbjct: 658 DSITTDHISPAGEIDPDYPAGKYLISKGVKEDDFNSYGSRRGNHEVMIRGTFGNIRIKNK 717

Query: 735 MLDGIEGGYAKKLPEGDVDFVYNVAMRYKAEGTPLLVIAGKEYGTGSSRDWAAKGTYLLG 794
           M++  EG +  K PE +  F+++ AM+Y+ E TPL+V AGKEYGTGSSRDWAAKGT LLG
Sbjct: 718 MVNR-EGSFTVKYPENEEMFIFDAAMKYQMENTPLVVFAGKEYGTGSSRDWAAKGTSLLG 776

Query: 795 IRAVLAESFERIHRSNLVGMGVLPLEFLPGENRETLGLTGYEVYDILGLEDLKPRKLVDI 854
           I+AV+AESFERIH+SNLVGMG+LPL+F  GE+     + G EV  I GLE+L PRK + I
Sbjct: 777 IKAVIAESFERIHKSNLVGMGILPLQFKEGESWAKYEIKGDEVVSIFGLENLSPRKDIRI 836

Query: 855 VARREDGSEVRFQAIARLDTPVEVDYYKNGGILQTVLLNML 895
              + DG +  F    RLDT VEV+YY NGGIL  VL   L
Sbjct: 837 ELSKPDGEKREFFVTLRLDTEVEVEYYANGGILPYVLRRFL 877


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: 2223
Number of extensions: 96
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: 877
Length adjustment: 43
Effective length of query: 859
Effective length of database: 834
Effective search space:   716406
Effective search space used:   716406
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