GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimF in Rhizobium etli CFN 42

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate WP_011423928.1 RHE_RS02825 FAD-dependent oxidoreductase

Query= metacyc::MONOMER-20678
         (699 letters)



>NCBI__GCF_000092045.1:WP_011423928.1
          Length = 738

 Score =  330 bits (847), Expect = 1e-94
 Identities = 239/736 (32%), Positives = 358/736 (48%), Gaps = 58/736 (7%)

Query: 11  DQVAIVTVDSP--PVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADIT-- 66
           D +A+VT D P   +N  +A V   +   ++A  AD +V+ +V      +F  GAD++  
Sbjct: 14  DGIALVTWDMPGKSMNVFTAEVMEELNAIIDATTADASVKGVVFTSGKSSFSGGADLSMI 73

Query: 67  ---------EFGKPPQPPA---------LNDVIAALENSPKPTIAAIHGTALGGGLEVAL 108
                    E  K P+            ++ +   LE S KP ++AI+GT +GG  E++L
Sbjct: 74  KSMFSSYQEEKAKSPEKAVQTLFGLVGRMSGLFRKLETSGKPWVSAINGTCMGGAFELSL 133

Query: 109 GCHFRVA--VKEAKLGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALK 166
            CH RVA   K  K+ LPEVK+G+ PGAGGTQR+PR    + A+QM+  G  +  + A  
Sbjct: 134 ACHGRVASNAKSVKIALPEVKVGIFPGAGGTQRVPRLANAQDALQMMTTGQSLSGSRAKA 193

Query: 167 HGLVEEVVE--NLVAGAVAFAKKVLAEKRPLRRLRDDDSKLAAA----KADRSIFTNAVA 220
             LV +VVE   L+  A    K  L   +P+    +   KL        A   ++  A A
Sbjct: 194 MNLVHQVVEPDQLIPAAKQMIKDGL---KPVAPWDEKGFKLPGGGIWTPASAQLWPAAPA 250

Query: 221 AMTKKARG-LEAPFACADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQ-RYAFFAER 278
            + ++  G   A  A    +   + +PF+ GLK E+  F +++ + ++ +  R  F + +
Sbjct: 251 ILRRETSGNYPAALAILKCVYEGLQVPFDTGLKIEQRYFTEVLQTREAFSMIRSLFISMQ 310

Query: 279 EAAKVDGVPDGTKPRPVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIM 338
           E  K    P G     +  V ++GAG MG  IA   A AGI VTLI+   E   +G  + 
Sbjct: 311 ELGKGARRPAGIPKTELKHVGVVGAGFMGASIAYVTAAAGISVTLIDRDMEAAAKGKAVS 370

Query: 339 QKNWEATAARGGLPPDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDA 398
           +   +    +G L  D  A  ++ IT      ++ +  L+IEAVFE   VKK V  AV+A
Sbjct: 371 EGLVKDAIGKGRLTQDEAAALLSRITPSGDYADLANVGLVIEAVFEDREVKKAVIDAVEA 430

Query: 399 HAKPGAVLASNTSYLSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLT 458
               GA+ ASNTS L I  +A  +KRP D +G+HFFSP   M L E++ G +T   AL  
Sbjct: 431 VLPEGAIFASNTSTLPITGLARNSKRPADFIGIHFFSPVEKMMLTEVILGTETGDRALAV 490

Query: 459 AVSIAKKIAKVPVVVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGP 518
           A+     I K P+VV    GF  NR +     +S  +L EG  P  ++      GMP+GP
Sbjct: 491 ALDYVAAIKKTPIVVNDTRGFFVNRCVLRYMSESYDMLIEGVPPAMIENAAKMAGMPVGP 550

Query: 519 FAMGDLAGLDIGWRSRK----DRGIKS------EIADALCE-AGRFGQKTGKGYYKYEQG 567
            A+ D   +D+  +  K    D G K+      E+   + E  GRFG+K  KG+Y Y   
Sbjct: 551 LALNDEVAIDLSLKILKAAVADLGEKAIDPRHMELISRMVEKEGRFGRKNSKGFYDYP-- 608

Query: 568 SRAPMPDPEVETLINDTLAKLGLKRRDITDEEIL-ERMVYPMINEGARILEEKIAARPSD 626
                P P  ++L  D  +    K+ +  D  +L +R +  +  E AR +EE I   P +
Sbjct: 609 -----PKPAKKSLWPDLKSFYPQKKAEEVDVNVLKQRFLVTIALEAARTVEEGIVTDPRE 663

Query: 627 IDVVWLYGYGWPIYRGGPMHYADSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGK 686
            DV  + G+G+  Y GG + Y D +G K   +     A+   D   +P PLL  LAA+G+
Sbjct: 664 ADVGSILGFGFAPYTGGALSYIDGMGAKAFVDLAERLAETYGD-HFKPTPLLRDLAAKGE 722

Query: 687 TFASLTQP---SKAAA 699
           TF     P   +KAAA
Sbjct: 723 TFYGRFDPYAGTKAAA 738


Lambda     K      H
   0.317    0.134    0.383 

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: 1078
Number of extensions: 56
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: 699
Length of database: 738
Length adjustment: 40
Effective length of query: 659
Effective length of database: 698
Effective search space:   459982
Effective search space used:   459982
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 (21.7 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Apr 09 2024. 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