Alignments for a candidate for acn in Coprobacter fastidiosus NSB1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Coprobacter fastidiosus NSB1

Align Aconitate hydratase A; ACN; Aconitase; EC 4.2.1.3; (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; EC 4.2.1.99; RNA-binding protein (uncharacterized)
to candidate WP_022599492.1 NSB1T_RS15930 aconitate hydratase

Query= curated2:Q68VV0
         (878 letters)



>NCBI__GCF_000473955.1:WP_022599492.1
          Length = 754

 Score =  205 bits (521), Expect = 9e-57
 Identities = 228/813 (28%), Positives = 348/813 (42%), Gaps = 136/813 (16%)

Query: 76  IDFMPARVLMQDFTGVPAIVDLAAMRDAMQKIGCNPLKINPLIPVDLVIDHSVSVDSYGL 135
           ++F P RV MQD T   A++    M     K+          +P  +  DH +  D    
Sbjct: 58  VNFSPDRVAMQDATAQMALLQF--MIAGKDKVA---------VPSSVHCDHLIQADI--- 103

Query: 136 KESFEQNVQMEMKRNIERYQFLKWGQQAFNNFKVV--PPGTGICHQVNLEYLSKVVWYND 193
                 +++  +  N E Y FLK      N + +    PG GI HQV LE          
Sbjct: 104 --DASNDIKKALVSNQEVYDFLK---DVSNKYGIGFWKPGAGIIHQVVLE---------- 148

Query: 194 GTAYPDSL-VGTDSHTTMVNGLSVLGWGVGGIEAEAAMLGQPLTMIIPEVIGVKLTGKLE 252
             A+P  + VGTDSHT    GL ++  GVGG +A   M G P  + +P++IGVKLTG+L 
Sbjct: 149 NYAFPGGMMVGTDSHTPNAGGLGMIAIGVGGADAVDVMTGIPWELKMPKIIGVKLTGELN 208

Query: 253 GMATATDLVLTITEMLRRTKVVGKFVEFFGYGLSNLTISDRATISNMSPEYGATCGFFPI 312
           G A+  D++L +  +L         +E+FG G  NL+ + +ATI NM  E GAT   F  
Sbjct: 209 GWASPKDVILKLAGILTVKGGTNAIIEYFGEGAKNLSATGKATICNMGAEVGATTSLFAY 268

Query: 313 DQETIKYLEITGRE---TRQIKLVEKYATEQNLWYNFEDTQEYTEVLELDLSTVYSSLAG 369
           D+   +YL+ TGRE       KL +    ++ +  N E  + Y  ++E++LS +   + G
Sbjct: 269 DESMARYLKATGREQIAEMANKLSDYLEADKEVIDNPE--KYYDRIIEINLSELEPYING 326

Query: 370 PKRPQDRVNLSFVESNFKNELPYFALENQDIDKKYAVANQNYEIGNGDVVIAAITSCTNT 429
           P  P     +S        E      EN           Q  E+G        I SCTN+
Sbjct: 327 PFTPDAAHPIS--------EFGRIVKENG--------YPQTMEVG-------LIGSCTNS 363

Query: 430 SNPSVMIGAALLAKKALEHGLNVKPWVKTSLAPGSKVVTEYLKISGLDKYLDALGFNLVG 489
           S   +   A++  + + +H   +K   +  + PGS+ V    +  GL    +++G  ++ 
Sbjct: 364 SYQDLSRAASVARQASKKH---LKAKAEFRINPGSEQVRYTAERDGLISDFESIGGIVMT 420

Query: 490 YGCTTCIGNSGSLNPEIENTINKNRLVVASVLSGNRNFEGRI--NPLTKASYLASPILVV 547
             C  CIG       + +   + N+   + V S NRNF  R   NP T A ++ASP +V 
Sbjct: 421 NACGPCIG-------QWKRHTDDNQRANSIVTSFNRNFAKRADGNPNTHA-FVASPEIVT 472

Query: 548 AYALSGTLNID-LTTTPIGAN-IYLKDIWPSQKEIDAVIANSINPSMFIEKYADVFNGTK 605
           A  ++G L  + LT T I  N   +K   P  +E+     +  +P      Y     G  
Sbjct: 473 ALTIAGNLCFNPLTDTLINENGESVKLDMPEGEELPVKGFDVKDPG-----YIAPDKGLS 527

Query: 606 EWHDLHITTGTNYNWDKNSTYINNPPYFDNICSENTIKDIKSAKILAIFGDSITTDHISP 665
              D+ I        D NS  +     F      N     +   +L       TTDHIS 
Sbjct: 528 S-SDIII--------DPNSKRLQKLSPFAPFNPLN----FERMPLLIKTSGKCTTDHISM 574

Query: 666 AGSISKNSPAAKYLIEHNIEPLNFNSYGSRRGNHEVMMRGTFANIRIKNEMCNGVEGGFT 725
           AG      P  ++    ++E ++ N          ++M    A     NE+         
Sbjct: 575 AG------PWLRF--RGHLENISDN----------LLMGAVNAFNGKTNEV--------- 607

Query: 726 INQLSGVQQTIYDAAMDYQAHDIPLVVFAGKEYGSGSSRDWAAKGPGLLGIKAIIAESFE 785
            NQL+    T+   A  Y+ H I  +V A + YG GSSR+ AA  P  LG+KA++ +SF 
Sbjct: 608 FNQLTNEYDTVSGTAKSYKMHGISSIVVAEENYGEGSSREHAALEPRFLGVKAVLCKSFA 667

Query: 786 RIHRSNLVGMGILPLTFTGNNTRLSLKLDGSETIDIIGLSKNIRPFNLVKCVIKKQTNEI 845
           RIH +NL   G+L LTF   +    +K    + + + GL       NL        T EI
Sbjct: 668 RIHETNLKKQGMLALTFVNKDDYNKIK--EKDILSVKGLESFAPDKNL--------TIEI 717

Query: 846 STIDLILQIFTEN------EINYIKHGSIMQFV 872
              D  L+ F  +      +I + K GS + ++
Sbjct: 718 IHPDGSLESFEASHTYNNLQIEWFKAGSALNYL 750


Lambda     K      H
   0.317    0.135    0.391 

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: 1546
Number of extensions: 77
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 878
Length of database: 754
Length adjustment: 41
Effective length of query: 837
Effective length of database: 713
Effective search space:   596781
Effective search space used:   596781
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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