GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Smeli:SM_b21632 SM_b21632 3-hydroxyacyl-CoA
           dehydrogenase
          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 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