Aligments for a candidate for acn in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Aligments for a candidate for acn in Azospirillum brasilense Sp245

Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; IP210; Iron-responsive protein-like; IRP-like; Major iron-containing protein; MICP; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate AZOBR_RS02985 AZOBR_RS02985 aconitate hydratase

Query= SwissProt::P37032
         (891 letters)



>FitnessBrowser__azobra:AZOBR_RS02985
          Length = 896

 Score = 1201 bits (3107), Expect = 0.0
 Identities = 593/890 (66%), Positives = 706/890 (79%), Gaps = 3/890 (0%)

Query: 4   GQDSLSTKSQLTVDGKTYNYYSLKEAENKHFKGINRLPYSLKVLLENLLRFEDGNTVTTK 63
           GQDSL T+  L+V GK+Y+Y+S+K AE+     ++RLPYS+KVLLENLLRFEDG TV+T 
Sbjct: 6   GQDSLKTRRSLSVGGKSYDYFSIKAAEDAGLGDLSRLPYSMKVLLENLLRFEDGRTVSTD 65

Query: 64  DIKAIADWLHNKTSQHEIAFRPTRVLMQDFTGVPAVVDLAAMRTAIVKMGGNADKISPLS 123
           D+KA+A WLH+K S  EIA+RP RVLMQDFTGVPAV DLAAMR A+  +GG+  KI+PL 
Sbjct: 66  DVKAVAQWLHDKRSDREIAYRPARVLMQDFTGVPAVCDLAAMREAMAALGGDPKKINPLV 125

Query: 124 PVDLVIDHSVMVDKFASADALEVNTKIEIERNKERYEFLRWGQKAFSNFQVVPPGTGICH 183
           PVDLVIDHSVMVD F +  A E N ++E ERN ERY FLRWGQKAF NF+VVPPGTGICH
Sbjct: 126 PVDLVIDHSVMVDYFGNPSAFEKNVELEFERNLERYAFLRWGQKAFDNFRVVPPGTGICH 185

Query: 184 QVNLEYLGKTVW-NSENDGQLYAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 242
           QVN+EYL + VW +++  G+L AYPDTLVGTDSHTTM+NGLGVLGWGVGGIEAEAAMLGQ
Sbjct: 186 QVNVEYLAQGVWTDTDPAGKLVAYPDTLVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQ 245

Query: 243 PVSMLIPEVIGFKLSGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGPGLNDLPLADR 302
           P+SMLIPEV+GFKL+G+LKEG TATDLVLTVTQMLRKKGVVGKFVEFYGPGL+ L LADR
Sbjct: 246 PISMLIPEVVGFKLTGRLKEGTTATDLVLTVTQMLRKKGVVGKFVEFYGPGLDHLTLADR 305

Query: 303 ATISNMAPEYGATCGFFPVDKETIKYLELTGRDKHTIALVEAYAKAQGMWYDKDNEEPVF 362
           ATI NMAPEYGATCG FP+D ETI+YL  TGRD   +A+VEAYA+AQGMW D    +PVF
Sbjct: 306 ATIGNMAPEYGATCGIFPIDAETIRYLTFTGRDADRVAMVEAYARAQGMWRDAGTPDPVF 365

Query: 363 TDSLHLDLGSVEPSLAGPKRPQDKVNLSSLPVEFNNFLIEVGKEKEKEKTFAVKNKDFQM 422
           TD+L LD+ +VEPSLAGPKRPQD+V LS     F   L+   K ++ +++  VK   + +
Sbjct: 366 TDALELDMTTVEPSLAGPKRPQDRVPLSQAAQSFGTDLVGAFKAEDADRSVPVKGCGYNL 425

Query: 423 KHGHVVIAAITSCTNTSNPSVLMAAGLVAKKAIEKGLQRKPWVKSSLAPGSKVVTDYLRH 482
             G VVIAAITSCTNTSNP+VL+AAGL+A+KA+EKGL+ KPWVK+SLAPGS+VVTDYL  
Sbjct: 426 DQGAVVIAAITSCTNTSNPAVLVAAGLLARKAVEKGLKSKPWVKTSLAPGSQVVTDYLAK 485

Query: 483 AGLQTYLDQLGFNLVGYGCTTCIGNSGPLPDDISHCVAEHDLVVSSVLSGNRNFEGRVHP 542
           AGLQ YLDQLGFN+VGYGCTTCIGNSGPLPD I+  V E +LVV++VLSGNRNFEGRV+P
Sbjct: 486 AGLQPYLDQLGFNIVGYGCTTCIGNSGPLPDPIAAAVEEGNLVVAAVLSGNRNFEGRVNP 545

Query: 543 QVRANWLASPPLVVAYALCGTTCSDLSREPIGQDKEGNDVYLKDIWPSNEEIAAEV-AKV 601
             RAN+LASPPL VAYAL G    DL+++PIG   +G  VYLKD+WP+N+E+   + A +
Sbjct: 546 HTRANYLASPPLCVAYALAGNMKIDLAKDPIGTGHDGQPVYLKDVWPTNQEVQDAIDASL 605

Query: 602 SGTMFRKEYAEVFKGDAHWQAIQTSSGQTYEWNPDSTYIQHPPFFENLSLKPEPLKPIKQ 661
           S  MFR  Y  VF+G   W+ IQT+ GQTYEW   STY++ PPFF ++   P+ +  ++ 
Sbjct: 606 SAEMFRSRYGNVFEGPEQWRGIQTAEGQTYEWQAGSTYVKLPPFFADMPKTPDAVSDVRG 665

Query: 662 AYVLALFGDSITTDHISPAGSIKASSPAGLYLKSKGVDEKDFNSYGSRRGNHEVMMRGTF 721
           A  LA+ GDSITTDHISPAGSIK +SPAG YL S  V  +DFNSYG+RRGNHEVMMRGTF
Sbjct: 666 ARALAVLGDSITTDHISPAGSIKKTSPAGEYLLSHQVRPQDFNSYGARRGNHEVMMRGTF 725

Query: 722 ANIRIRNEMTPGQEGGVTRYVPTGETMSIYDAAMRYQENQQDLVIIAGKEYGTGSSRDWA 781
           ANIRIRNEM  G EGG TR+ P+GE + IY AAMRY +    LV+IAGKEYGTGSSRDWA
Sbjct: 726 ANIRIRNEMLAGVEGGETRHYPSGEQLPIYTAAMRYAQEGVPLVVIAGKEYGTGSSRDWA 785

Query: 782 AKGTNLLGVKAVITESFERIHRSNLIGMGILPLQFKEGTTRKTLKLDGSERISIE-ISDK 840
           AKGT LLG++AVI ESFERIHRSNL+GMGILPLQFK+G TR  L LDG+E   I+ I   
Sbjct: 786 AKGTKLLGIRAVIAESFERIHRSNLVGMGILPLQFKDGLTRNDLALDGTETFDIDGIEQD 845

Query: 841 LTPGAMVPVTIERQDGDIEKIETLCRIDTADELEYYKNGGILQYVLRKIS 890
           L P   V +TI R DG   ++  L RIDT DE+EYY+NGG+L +VLR ++
Sbjct: 846 LRPRKDVTMTITRADGQTRQVPLLLRIDTVDEVEYYRNGGVLNFVLRNLA 895


Lambda     K      H
   0.316    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: 2142
Number of extensions: 82
Number of successful extensions: 4
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: 891
Length of database: 896
Length adjustment: 43
Effective length of query: 848
Effective length of database: 853
Effective search space:   723344
Effective search space used:   723344
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 17 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, or view the source code.

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