GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astD in Marinobacter adhaerens HP15

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate GFF1133 HP15_1111 betaine aldehyde dehydrogenase

Query= reanno::MR1:199807
         (487 letters)



>lcl|FitnessBrowser__Marino:GFF1133 HP15_1111 betaine aldehyde
           dehydrogenase
          Length = 493

 Score =  182 bits (463), Expect = 2e-50
 Identities = 152/487 (31%), Positives = 236/487 (48%), Gaps = 45/487 (9%)

Query: 3   HFIKGQWHTGKGHDVASS-NPANGEIIWRGQTATAEQVNAAVDAAREA-QFDWFILGFDA 60
           H I GQ+ +     +  + NPANG+II +   A  E+V+AAV AAR A +  W  +  D 
Sbjct: 13  HHINGQYVSSCSSRLFDNVNPANGKIISKVHEAGREEVDAAVKAARAALRGPWGKMTLDE 72

Query: 61  RLKIVEAYRSQLEANKAELAETIAQETGKPQWETATEVAAMIGKIGLSASAYN------- 113
           R  I+      + A   E  E    +TGKP+        +M   I +   A N       
Sbjct: 73  RTSILHKVADGINARFDEFLEGECLDTGKPK--------SMASHIDIPRGAANFKVFADM 124

Query: 114 -KRTGTETND--TPAGRAVLRH---KPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVVF 167
            K   TE+ +  TP G   L +   +P GV+ V  P+N P  L    + PAL  GN+VV 
Sbjct: 125 IKNVPTESFEMPTPDGTGALNYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVV 184

Query: 168 KPSELTPKVAELMVTLWEKSGLPAGVLNLVQ--GEVDTGKALASHPQLDGLFFTGSSRTG 225
           KPSE TP    L+  + +++G+P GV N+V   G    G  L  HPQ+DG+ FTG   TG
Sbjct: 185 KPSEETPTTTTLLGEVMKEAGVPDGVFNVVHGFGGDSAGAFLTEHPQVDGITFTGEIGTG 244

Query: 226 HLLHQQYAGHPGKILALEMGGNNPLIIKGVADIKAAVHDILQSAYISSGQRCTCARRLYV 285
            ++  + A    + ++LE+GG N  ++    DI  A+   ++SA+ + GQ C    R+YV
Sbjct: 245 EVI-MKAAAKGIRDISLELGGKNAGVVFADCDIDKAIEGTMRSAFANCGQVCLGTERVYV 303

Query: 286 EQGEQGDALVAKLVEAVKQIKVGPWNAQPQPFMGSMISEAAAKGMVAAQ-------ANLL 338
           E+    D  V +L EA + +K+GP +   +  MG ++S    + +++         A ++
Sbjct: 304 ER-SIFDEFVGRLKEAAEGMKIGPPD-DAEADMGPLVSLNHREKVLSYYQKAVDDGATVV 361

Query: 339 SLGGVPLVELMHLQAGTGLVSP----GLIDVTAVSELPDEEYFGPLLQLVRYSDFDQAIK 394
           + GGVP  E+    AG   V P    GL + +AV     +E FGP   +  +   ++AI+
Sbjct: 362 TGGGVP--EMPEALAGGAWVQPTIWTGLPEDSAVI---TDEIFGPCCHIRPFDTEEEAIE 416

Query: 395 LANQTRYGLSAGILADSREDYEYFLARIRAGIVNWNKQITGASGAAPFGGVGASGNHRAS 454
           LAN   YGL++ I +++         +I AGI+ W           PFGG   SG  R  
Sbjct: 417 LANSLPYGLASAIWSENITRAHRVAGQIEAGII-WVNSWFLRDLRTPFGGSKQSGIGREG 475

Query: 455 AFYAADY 461
             ++ ++
Sbjct: 476 GVHSLEF 482


Lambda     K      H
   0.316    0.133    0.391 

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: 603
Number of extensions: 41
Number of successful extensions: 6
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: 487
Length of database: 493
Length adjustment: 34
Effective length of query: 453
Effective length of database: 459
Effective search space:   207927
Effective search space used:   207927
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 (21.6 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 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