GapMind for catabolism of small carbon sources

 

Alignments 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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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:

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:

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:

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:

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