Alignments for a candidate for acn in Belnapia rosea CPCC 100156

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Belnapia rosea CPCC 100156

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_090661743.1 BLR02_RS06435 aconitate hydratase AcnA

Query= SwissProt::P70920
         (906 letters)



>NCBI__GCF_900101615.1:WP_090661743.1
          Length = 898

 Score = 1147 bits (2967), Expect = 0.0
 Identities = 580/908 (63%), Positives = 693/908 (76%), Gaps = 18/908 (1%)

Query: 1   MTSLDSFKCKKTLKVGAKTYVYYSLPTAEKNGLKGISKLPYSMKVLLENLLRNEDGRSVK 60
           M   DS K ++TL+V  KTY Y+SLP A ++ +  I++LPYS+KVLLEN+LR EDGRS  
Sbjct: 3   MIGQDSLKTRRTLEVDGKTYHYFSLPEAARS-IGDIARLPYSLKVLLENILRYEDGRSYT 61

Query: 61  KADIVAVSKWLRKKSLEHEIAFRPARVLMQDFTGVPAVVDLAAMRNAMQKLGGDAEKINP 120
             D  +++ WL     + E+ FRP+R+LMQDFTGVPAVVDLAAMR+ +  LGGD  K+NP
Sbjct: 62  VDDAKSIAGWLPSGHSDKEVPFRPSRILMQDFTGVPAVVDLAAMRDGIIALGGDPRKVNP 121

Query: 121 LVPVDLVIDHSVIVNFFGDNKAFAKNVTEEYKQNQERYEFLKWGQAAFSNFSVVPPGTGI 180
           LVPVDLVIDHSV+V+  G  +A  +NV  E+++N ERYEFL+WGQAAF NF VVPPGTGI
Sbjct: 122 LVPVDLVIDHSVMVDVSGTPQALQRNVDIEFQRNGERYEFLRWGQAAFDNFRVVPPGTGI 181

Query: 181 CHQVNLEYLSQTVWTKKEKMTVGKKTGTFEVAYPDSLVGTDSHTTMVNGLAVLGWGVGGI 240
           CHQVNLEYL+Q  WT ++   +G         YPDS  GTDSHTTMVNGL VLGWGVGGI
Sbjct: 182 CHQVNLEYLAQVAWTSQD---IGDT-----YVYPDSCYGTDSHTTMVNGLGVLGWGVGGI 233

Query: 241 EAEACMLGQPLSMLLPNVVGFKLKGAMKEGVTATDLVLTVTQMLRKLGVVGKFVEFFGPG 300
           EAEA MLGQP++ML+P+V+GFKL G ++EGVTATDLVLTVTQMLRK GVVGKFVEFFGPG
Sbjct: 234 EAEAAMLGQPIAMLIPDVIGFKLTGKLREGVTATDLVLTVTQMLRKKGVVGKFVEFFGPG 293

Query: 301 LDHLSVADKATIANMAPEYGATCGFFPVDAAAIDYLKTSGRAAPRVALVQAYAKAQGLFR 360
           LD L +AD+ATI NMAPEYGATCGFFPVDA  I YL+ SGR   R+ LV+AYAKAQG++R
Sbjct: 294 LDDLPLADRATIGNMAPEYGATCGFFPVDAVTIGYLRLSGREEHRIKLVEAYAKAQGMWR 353

Query: 361 TAKSADPVFTETLTLDLADVVPSMAGPKRPEGRIALPSVAEGFSVALANEYKKT--EEPA 418
            + S DPVFT+TL LD+A V PS+AGPKRP+ R+AL + A  F+  LA        +E  
Sbjct: 354 DSSSPDPVFTDTLELDMATVEPSLAGPKRPQDRVALSNAATSFAKDLAAGTMGVPGDEAT 413

Query: 419 KRFAVEGKKYEIGHGDVVIAAITSCTNTSNPSVLIGAGLLARNAAAKGLKAKPWVKTSLA 478
           KR  VEG  Y++GHGDVVIAAITSCTNTSNP V++ AGL+AR A  KGL  KPWVKTSLA
Sbjct: 414 KRVPVEGANYDLGHGDVVIAAITSCTNTSNPYVMVAAGLVARKAREKGLAPKPWVKTSLA 473

Query: 479 PGSQVVAAYLADSGLQAHLDKVGFNLVGFGCTTCIGNSGPLPEEISKSINDNGIVAAAVL 538
           PGSQVV  Y   SGLQA LD +GF  VG+GCTTCIGNSGPLP+ I  +I +N +VAA+VL
Sbjct: 474 PGSQVVTEYFEKSGLQADLDAIGFQTVGYGCTTCIGNSGPLPDPIVDAIENNKLVAASVL 533

Query: 539 SGNRNFEGRVSPDVQANYLASPPLVVAHALAGSVTKNLAVEPLGEGKDGKPVYLKDIWPT 598
           SGNRNFEGRV  +V+ANYLASPPLVVA+ALAG++TK++  EP+G G DG+PVYLKDIWPT
Sbjct: 534 SGNRNFEGRVHANVRANYLASPPLVVAYALAGTITKDITKEPIGTGSDGQPVYLKDIWPT 593

Query: 599 SKEINAFMKKFVTASIFKKKYADVFKGDTNWRKIKT-VESETYRWNMSSTYVQNPPYFEG 657
            KE+N  +   VT  +F+ +Y DVFKG   W+ I+   +S+TYRWN  STYVQNPPYFEG
Sbjct: 594 QKEVNDTVHACVTREMFQGRYGDVFKGPEQWQAIRVDADSDTYRWNSGSTYVQNPPYFEG 653

Query: 658 MKKEPEPVTDIVEARILAMFGDKITTDHISPAGSIKLTSPAGKYLSEHQVRPADFNQYGT 717
           M  + +PVT +  AR+LA   D ITTDHISPAG+I+  SPAG+YL EHQVR  DFN YG 
Sbjct: 654 MSADIKPVTSVHGARVLAELADSITTDHISPAGNIRKASPAGEYLVEHQVRQDDFNSYGA 713

Query: 718 RRGNHEVMMRGTFANIRIKNFMLKGADGNIPEGGLTKHWPDGEQMSIYDAAMKYQQEQVP 777
           RRGNHEVMMRGTFANIRIKN M+ G      EGG++KH+P G+   IY+ AM+Y+ E VP
Sbjct: 714 RRGNHEVMMRGTFANIRIKNEMVPGT-----EGGISKHYPSGDVAPIYNVAMRYKAEGVP 768

Query: 778 LVVFAGAEYGNGSSRDWAAKGTRLLGVRAVICQSFERIHRSNLVGMGVLPLTFEEGTSWS 837
           LVVF G EYG GSSRDWAAKGT LLGV+AVI +SFERIHRSNLVGMGVLPL F  G    
Sbjct: 769 LVVFGGKEYGTGSSRDWAAKGTFLLGVKAVIAESFERIHRSNLVGMGVLPLVFMNGEDRK 828

Query: 838 SLGLKGDEKVTLRGLVGDLKPRQKLTAEIVSGDGSLQRVSLLCRIDTLDELDYYRNGGIL 897
           SLG++GDE + + GL   L PRQ L   I   DG+  R  +L RIDT DE++YY+NGGIL
Sbjct: 829 SLGIQGDEVIDILGL-EQLSPRQTLELVIRRADGTETRTKVLSRIDTADEVEYYKNGGIL 887

Query: 898 HYVLRKLA 905
           HYVLR +A
Sbjct: 888 HYVLRGMA 895


Lambda     K      H
   0.317    0.134    0.393 

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: 2179
Number of extensions: 84
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: 906
Length of database: 898
Length adjustment: 43
Effective length of query: 863
Effective length of database: 855
Effective search space:   737865
Effective search space used:   737865
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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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