GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaH in Sinorhizobium meliloti 1021

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate SM_b21632 SM_b21632 3-hydroxyacyl-CoA dehydrogenase

Query= reanno::BFirm:BPHYT_RS13545
         (706 letters)



>lcl|FitnessBrowser__Smeli:SM_b21632 SM_b21632 3-hydroxyacyl-CoA
           dehydrogenase
          Length = 438

 Score =  351 bits (900), Expect = e-101
 Identities = 195/425 (45%), Positives = 267/425 (62%), Gaps = 11/425 (2%)

Query: 276 LIHAFFAEREVLKAPETRAAKPRTLNTIGVVGGGTMGAGIAVAVLDAGLPVTMIERDDAS 335
           L + F AER     P     +PR + +  V+GGGTMG GIA A+L AGLP+ ++ERD+A+
Sbjct: 20  LRYVFHAERAARHPPALAGIEPRPIRSAAVIGGGTMGTGIAAALLHAGLPLVLVERDEAA 79

Query: 336 LARGRAHIEKVYDGLIAKGRLSAEKKAALMSRWSGSTSYDALAGADLVIEAVFEDLAVKQ 395
           + R  A +  ++DG + +GR+SA   A  ++  +GST Y A+A ADL+IEAVFEDL VK+
Sbjct: 80  VERALARLRTIFDGAVKRGRISAGLAAERLAGVTGSTDYTAIAEADLIIEAVFEDLDVKR 139

Query: 396 AVFAELDRVCKAGAVLATNTSYLDIDALASSVSRPADVIGLHFFSPANIMKLLEVVVPKQ 455
            VF  L  VC+A A+LATNTSYLD + +A+ +      +GLHFFSPA +MKLLE+V  + 
Sbjct: 140 DVFRRLAAVCRADAILATNTSYLDPERIAADIGSRERFLGLHFFSPAQVMKLLEIVPTQA 199

Query: 456 VSADVVATAFELAKKLRKTPVRAGVCDGFIGNRVLAVYRSAADAMMEDGASPYQIDAAVR 515
            + DV+AT F LA+ L K PVRAG+ DGFIGNR+L V R+ A+ ++  GA+P  +DAA+R
Sbjct: 200 TAPDVLATGFALARMLNKIPVRAGISDGFIGNRILKVTRAQAERLLLSGATPAAVDAAMR 259

Query: 516 AFGFPMGPFQVVDLAGGDIGWAARKRRAATRNPAARYVQIADRLCERGWFGQKSGRGFYL 575
           AFG PMGPF+  DL G DI  AA +RRAA       +  +ADRL     FGQKSG G+Y 
Sbjct: 260 AFGLPMGPFEAQDLGGLDI--AAFQRRAARARGETTFAPVADRLSAIERFGQKSGGGWYD 317

Query: 576 YPEGSRSGTPDPEVEAIIDAERARAGITPRSFTDEEIIRRYMAAMINEGANVVHERIALR 635
           Y  G R+  P   V  II AE AR G   R + +  I+   +  M+NE A ++ +  ALR
Sbjct: 318 YAPGDRTPRPSATVARII-AEEAR-GWPRRDWDEASIVGCILWPMVNEAARILEDGTALR 375

Query: 636 PLDVDVTFLYGYGFPRYRGGPMKYADMVGLPKI---LADIREFAKEDPLFWKPSPLLIEL 692
             D+D+  ++GYGFPR+RGG M +A+  GL K+   L+ + E    DP    P   L+  
Sbjct: 376 ASDIDLVEIHGYGFPRWRGGLMHHAEAHGLHKVAGALSGLAEAGLADP----PCDPLLRA 431

Query: 693 VERGA 697
             RG+
Sbjct: 432 ASRGS 436


Lambda     K      H
   0.320    0.136    0.392 

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: 764
Number of extensions: 30
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: 706
Length of database: 438
Length adjustment: 36
Effective length of query: 670
Effective length of database: 402
Effective search space:   269340
Effective search space used:   269340
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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