GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dino:3609503
          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 (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