GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Marino:GFF1133
          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:

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