GapMind for catabolism of small carbon sources

 

Aligments for a candidate for praB in Dinoroseobacter shibae DFL-12

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate 3609503 Dshi_2887 succinic semialdehyde dehydrogenase (RefSeq)

Query= BRENDA::Q1XGK8
         (486 letters)



>lcl|FitnessBrowser__Dino:3609503 Dshi_2887 succinic semialdehyde
           dehydrogenase (RefSeq)
          Length = 492

 Score =  313 bits (803), Expect = 7e-90
 Identities = 177/482 (36%), Positives = 260/482 (53%), Gaps = 10/482 (2%)

Query: 5   KHFINGAFVGSASGRTFEDINPSNGQVIGHVHEAGRAEVDAAVKAARAALKGPWGKLSVA 64
           K +  GA+  + SG TF   NP+ G VI HV + GRAE   A+ AA AA K PW   +  
Sbjct: 21  KAYFAGAWTDADSGATFPVTNPARGDVIAHVPDLGRAETARAIAAADAAQK-PWAARTAK 79

Query: 65  ERAEILHRVADGITARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADLLKNVANE 124
           +RA++L R  D I    D+       + GKP + A   ++  GA+  + FA+  K +  E
Sbjct: 80  DRAQVLRRWFDLIVGNADDLARILTAEMGKPLAEARG-EVMYGASFVEWFAEEAKRLYGE 138

Query: 125 AFEMATPDGAGAINYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSEETP 184
                 PD    +   +R+P GV+G I+PWN P+ ++T K  PALA G   + KP+E+TP
Sbjct: 139 TIPGHLPDARIQV---IRQPIGVVGAITPWNFPIAMITRKAAPALAAGCAFLSKPAEDTP 195

Query: 185 LTATLLGEVMQAAGVPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGEVIMRAA 244
           L+A  L  + + AG+PAG++ V+      + G    E+  V   TFTG T  G +++  A
Sbjct: 196 LSALALAVLAERAGIPAGLFAVLPSSDSSAIGKEFCENHTVRKLTFTGSTQVGRILLAQA 255

Query: 245 AKGVRQVSLELGGKNAGIVFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPIFDEF 304
           A  V++ S+ELGG    IVF D D+DKA+EG +   F N GQ C+   R+YV+  ++D F
Sbjct: 256 ADQVKKCSMELGGNAPFIVFDDADLDKAVEGAMACKFRNAGQTCVCANRIYVQDGVYDAF 315

Query: 305 VARLKAGAESLMIGPPDDASSNFGPLVSLKHREKVLSYYQQAVDDGGSVITGGGVPDMPA 364
             +L A  E L +G         GPL+++   EKV  +       GG+V+TGG       
Sbjct: 316 AEKLAAAVEELKVGDGAAEGVTIGPLINMPAVEKVQDHLDDLRAKGGTVVTGG-----ET 370

Query: 365 HLAGGAWVQPTIWTGLSDDSAVVTEEIFGPCCHIRPFDTEEEAIELANSLPYGLASAIWT 424
           H  GG +  PT+ TG++ +  V  EE FGP   +  F  E+E I +AN   +GLA   + 
Sbjct: 371 HPLGGTFFTPTVVTGVTQEMKVAREETFGPVAPLFRFTEEDEVIAMANDTIFGLAGYFYA 430

Query: 425 ENGSRAHRVAGQIEAGIVWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNICV 484
            +  R  RV+  +E GIV +N+  +      FGG KQSG+GREG  H ++ Y E+K IC+
Sbjct: 431 RDIGRITRVSEALEYGIVGINTGIISTEGAPFGGVKQSGLGREGSRHGIDEYLEMKYICL 490

Query: 485 KL 486
            +
Sbjct: 491 SI 492


Lambda     K      H
   0.318    0.136    0.411 

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: 626
Number of extensions: 32
Number of successful extensions: 4
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: 486
Length of database: 492
Length adjustment: 34
Effective length of query: 452
Effective length of database: 458
Effective search space:   207016
Effective search space used:   207016
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: 52 (24.6 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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