GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimF in Sinorhizobium meliloti 1021

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate SM_b21632 SM_b21632 3-hydroxyacyl-CoA dehydrogenase

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



>FitnessBrowser__Smeli:SM_b21632
          Length = 438

 Score =  322 bits (825), Expect = 2e-92
 Identities = 184/421 (43%), Positives = 253/421 (60%), Gaps = 12/421 (2%)

Query: 271 RYAFFAEREAAKVDGVPDGTKPRPVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQ 330
           RY F AER AA+      G +PRP+   A+IG GTMG GIA +  +AG+P+ L+E  E  
Sbjct: 21  RYVFHAER-AARHPPALAGIEPRPIRSAAVIGGGTMGTGIAAALLHAGLPLVLVERDEAA 79

Query: 331 LKRGLGIMQKNWEATAARGGLPPDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKK 390
           ++R L  ++  ++    RG +     A+R+A +TG      + +ADLIIEAVFE + VK+
Sbjct: 80  VERALARLRTIFDGAVKRGRISAGLAAERLAGVTGSTDYTAIAEADLIIEAVFEDLDVKR 139

Query: 391 EVFTAVDAHAKPGAVLASNTSYLSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAK 450
           +VF  + A  +  A+LA+NTSYL  + IAA     +  LG+HFFSPA VMKL EIV    
Sbjct: 140 DVFRRLAAVCRADAILATNTSYLDPERIAADIGSRERFLGLHFFSPAQVMKLLEIVPTQA 199

Query: 451 TAPDALLTAVSIAKKIAKVPVVVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVT 510
           TAPD L T  ++A+ + K+PV  G+ DGF+GNR+L     Q+E+LL  GA P  VDA + 
Sbjct: 200 TAPDVLATGFALARMLNKIPVRAGISDGFIGNRILKVTRAQAERLLLSGATPAAVDAAMR 259

Query: 511 KFGMPMGPFAMGDLAGLDIGWRSRKDRGIKSE-----IADALCEAGRFGQKTGKGYYKYE 565
            FG+PMGPF   DL GLDI    R+    + E     +AD L    RFGQK+G G+Y Y 
Sbjct: 260 AFGLPMGPFEAQDLGGLDIAAFQRRAARARGETTFAPVADRLSAIERFGQKSGGGWYDYA 319

Query: 566 QGSRAPMPDPEVETLINDTLAKLGLKRRDITDEEILERMVYPMINEGARILEEKIAARPS 625
            G R P P   V  +I +     G  RRD  +  I+  +++PM+NE ARILE+  A R S
Sbjct: 320 PGDRTPRPSATVARIIAEEAR--GWPRRDWDEASIVGCILWPMVNEAARILEDGTALRAS 377

Query: 626 DIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAERLSAYAKA-TNDPSLEPAPLLARLAAE 684
           DID+V ++GYG+P +RGG MH+A++ GL  +A  LS  A+A   DP  +P   L R A+ 
Sbjct: 378 DIDLVEIHGYGFPRWRGGLMHHAEAHGLHKVAGALSGLAEAGLADPPCDP---LLRAASR 434

Query: 685 G 685
           G
Sbjct: 435 G 435


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: 696
Number of extensions: 36
Number of successful extensions: 3
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: 438
Length adjustment: 36
Effective length of query: 663
Effective length of database: 402
Effective search space:   266526
Effective search space used:   266526
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: 53 (25.0 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