GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Marivita geojedonensis DPG-138

Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_085640679.1 MGEO_RS17260 betaine-aldehyde dehydrogenase

Query= reanno::pseudo6_N2E2:Pf6N2E2_4383
         (497 letters)



>NCBI__GCF_002115805.1:WP_085640679.1
          Length = 485

 Score =  339 bits (870), Expect = 1e-97
 Identities = 189/487 (38%), Positives = 289/487 (59%), Gaps = 16/487 (3%)

Query: 15  DLKIEGRAFINGEYTDAVSGETFDCLSPVDGRLLGKIASCDVADAQRAVENARATFSSGV 74
           D + +   FI+G Y +  +G     + P  G  +  + +   A   +A+  A A  +   
Sbjct: 4   DTQPKASHFIDGAYVEDTTGTPIPVIYPATGEQIATVYAATPAIVDKAL--AAAHRAQKA 61

Query: 75  WSRLAPSKRKATMIRFAGLLKQHAEELALLETLDMGKPISDSLNIDVPGAAQALSWSGEA 134
           W+ ++ ++R   + R A ++++   +L++LET D GKP  +++ +D    A AL + G  
Sbjct: 62  WAAMSGTERGRILRRAADMMRERNHDLSVLETYDTGKPYQETIAVDATSGADALEYFGGL 121

Query: 135 IDKLYDEVAATPHDQLG----LVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVVL 190
              L  E     H QLG       REP+GV   I  WN+P  +ACWK  PAL+ GN++V 
Sbjct: 122 AGSLTGE-----HIQLGEDWVYTRREPLGVCVGIGAWNYPTQIACWKGAPALACGNAMVF 176

Query: 191 KPSEKSPLTALRIAALAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAK 250
           KPSE +PL AL++A +  EAG+P G+ NV+ G G  VG +L     V  +  TGS    K
Sbjct: 177 KPSETTPLCALKVAEILHEAGLPAGIYNVVQGLGE-VGASLVTDPRVAKVSLTGSVPTGK 235

Query: 251 QLMIYSGESNMKRIWLEAGGKSPNIVFADAPDLQAAAESAASAIAFNQGEVCTAGSRLLV 310
           ++   + E  MK + +E GGKSP ++F DA DL+ A   A     ++ G+VC+ G+R+ V
Sbjct: 236 KVYAAAAEQ-MKHVTMELGGKSPLLIFDDA-DLENAVGGAILGNFYSSGQVCSNGTRVFV 293

Query: 311 ERSIKDTFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHSDGAKLVAG 370
           ++ IK+ FL  + E L     G+PLD ATN G +V  +QM  VL YIE G ++GA+LVAG
Sbjct: 294 QKGIKEAFLKRLTERLSTAVVGDPLDEATNFGPMVSEKQMKIVLDYIEKGENEGARLVAG 353

Query: 371 GKRILEETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIAFDTAEQAIEIANDTPYGLA 430
           G+R+  +  G Y++PT+F  V + M IA+EEIFGPV++V+ F+T E+AI  AN T +GL+
Sbjct: 354 GRRLNRD--GFYLQPTVFADVKDDMIIAREEIFGPVMAVLDFETEEEAITRANSTEFGLS 411

Query: 431 AAVWTKDISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTEL 490
           A V+T+D+S+AH     L AGS ++N Y+   + APFGG K SG GR+ S  A + Y+E+
Sbjct: 412 AGVFTRDLSRAHRVIAQLEAGSCFINSYNDAPVEAPFGGTKMSGVGRENSKAAINHYSEM 471

Query: 491 KSTWIKL 497
           KS ++++
Sbjct: 472 KSVYVRM 478


Lambda     K      H
   0.316    0.132    0.389 

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: 583
Number of extensions: 26
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: 497
Length of database: 485
Length adjustment: 34
Effective length of query: 463
Effective length of database: 451
Effective search space:   208813
Effective search space used:   208813
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 24 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