GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimF in Arenimonas metalli CF5-1

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate WP_034210667.1 N787_RS02965 3-hydroxyacyl-CoA dehydrogenase

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



>NCBI__GCF_000747155.1:WP_034210667.1
          Length = 680

 Score =  267 bits (683), Expect = 1e-75
 Identities = 209/669 (31%), Positives = 316/669 (47%), Gaps = 48/669 (7%)

Query: 11  DQVAIVTVDSPP--VNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEF 68
           D + ++T+D     VNALS AV   +   V     +     +++      FI GADI  F
Sbjct: 21  DGILVLTLDRADQNVNALSRAVLDELESMVERIALELPKGVVIISGKAAGFIPGADIKGF 80

Query: 69  GKPPQPPALND-------VIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAK- 120
           G         D       V   L     PT+AAIHG  +GGG E++L C +R+A  + K 
Sbjct: 81  GDIAAKGQTEDWIRHGQLVFQKLAELRCPTVAAIHGHCMGGGTEISLACRYRIASNDEKT 140

Query: 121 -LGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVENLVA 179
            +GLPEVKLG+ PG GG+ R PR +G   A+ +++ G  + A+ A   GLV++VV    A
Sbjct: 141 RIGLPEVKLGIYPGWGGSVRAPRLLGAPAAMDLMLTGRSLSASAARAIGLVDKVV----A 196

Query: 180 GAVAFAKKV-LAEKRPLRRLRDDDSKLAAAKAD-RSIFTNAVAA-MTKKARG--LEAPFA 234
            AV   + V LA++   R  +      A      R++    +A  + +KAR     APFA
Sbjct: 197 PAVLLDEAVKLAQRGTTRPFKQRFLAWATNTGPGRALLAPQIAKQVARKARKEHYPAPFA 256

Query: 235 CADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRP 294
             +    +  LP    LK E +  +KL  +  +      FF       + G   G     
Sbjct: 257 LIETWRRSGGLPVHAALKAEAKSVVKLAATPTAHNLVRVFFLMDRLKSLGGKDHG----- 311

Query: 295 VSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPD 354
           +S+V +IGAG MGG IA   A  G  VTL +   + ++  L    K +E           
Sbjct: 312 ISKVHVIGAGVMGGDIAAWCALRGFEVTLQDREMKYIQPALDRAAKLFEKKVKDEAKRAA 371

Query: 355 APAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLS 414
             A+  A + G      V DADL+IEA+FE +  K+ +F  V+   KPGA+L SNTS + 
Sbjct: 372 TSARLKADVEGT----GVADADLVIEAIFENLEAKQALFAKVEETLKPGAILVSNTSSIP 427

Query: 415 IDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVG 474
           + ++ A  K P    G+H+F+P  +M L EIVR      +      +  K I K+PV V 
Sbjct: 428 LTDLRAGRKDPARFAGLHYFNPVALMPLVEIVRHDGLDAETERRLAAFCKAIDKLPVPVA 487

Query: 475 VCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSR 534
              GF+ NR+LA   +++     EG     +D V  KFGMPMGP  + D  GLD+     
Sbjct: 488 GTPGFLVNRILAPYMQEAIVAFSEGIPGPVIDKVALKFGMPMGPIELVDTVGLDVAASVG 547

Query: 535 KDRG--IKSEIADAL-CEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLK 591
           K         + DA   E G+ G+K G+G YK+E G RA  P+               + 
Sbjct: 548 KIMADFHGQPLPDAFKVEDGKRGKKDGQGLYKWENG-RAVKPE---------------VP 591

Query: 592 RRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSV 651
           +     E++ +R++ P++NE    L + + +    +D   ++G G+  +RGGP+ +  +V
Sbjct: 592 KDYQAPEDLEDRLILPLLNEAVSCLHDGVVSDADLLDAGVIFGTGFAPFRGGPIQHIKAV 651

Query: 652 GLKHIAERL 660
           G   +  RL
Sbjct: 652 GADKLKARL 660


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: 1094
Number of extensions: 61
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: 680
Length adjustment: 39
Effective length of query: 660
Effective length of database: 641
Effective search space:   423060
Effective search space used:   423060
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: 54 (25.4 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:

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