GapMind for catabolism of small carbon sources

 

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

Align 2-aminomuconic 6-semialdehyde dehydrogenase; Aminomuconate-semialdehyde dehydrogenase; EC 1.2.1.32 (characterized)
to candidate WP_085640679.1 MGEO_RS17260 betaine-aldehyde dehydrogenase

Query= SwissProt::Q9KWS5
         (491 letters)



>NCBI__GCF_002115805.1:WP_085640679.1
          Length = 485

 Score =  313 bits (802), Expect = 9e-90
 Identities = 185/487 (37%), Positives = 263/487 (54%), Gaps = 16/487 (3%)

Query: 6   NFVDGKWVESSK--TFQDVTPIDGSVVAVVHEADRDLVDAAVKAGHRALEGEWGRTTAAQ 63
           +F+DG +VE +       + P  G  +A V+ A   +VD A+ A HRA +  W   +  +
Sbjct: 11  HFIDGAYVEDTTGTPIPVIYPATGEQIATVYAATPAIVDKALAAAHRAQKA-WAAMSGTE 69

Query: 64  RVDWLRRIANEMERRQQDFLDAEMADTGKPLSMAATIDIPRGIANFRNFADILATAPVDS 123
           R   LRR A+ M  R  D    E  DTGKP      +D   G      F  +  +  +  
Sbjct: 70  RGRILRRAADMMRERNHDLSVLETYDTGKPYQETIAVDATSGADALEYFGGLAGS--LTG 127

Query: 124 HRLDLPDGAYALNYAARKPLGVVGVISPWNLPLLLLTWKVAPALACGNAVVVKPSEDTPG 183
             + L +      Y  R+PLGV   I  WN P  +  WK APALACGNA+V KPSE TP 
Sbjct: 128 EHIQLGEDWV---YTRREPLGVCVGIGAWNYPTQIACWKGAPALACGNAMVFKPSETTPL 184

Query: 184 TATLLAEVMEAVGIPPGVFNLVHGFGPNSAGEFISQHPDISAITFTGESKTGSTIMRAAA 243
            A  +AE++   G+P G++N+V G G    G  +   P ++ ++ TG   TG  +  AAA
Sbjct: 185 CALKVAEILHEAGLPAGIYNVVQGLG--EVGASLVTDPRVAKVSLTGSVPTGKKVYAAAA 242

Query: 244 EGVKPVSFELGGKNAAVIFADCDFEKMLDGMMRALFLNSGQVCLCSERVYVERPIFDRFC 303
           E +K V+ ELGGK+  +IF D D E  + G +   F +SGQVC    RV+V++ I + F 
Sbjct: 243 EQMKHVTMELGGKSPLLIFDDADLENAVGGAILGNFYSSGQVCSNGTRVFVQKGIKEAFL 302

Query: 304 VALAERIKALKVDWPHETDTQMGPLISSKHRDKVLSYFELARQEGATFLAGGGVPRFGDE 363
             L ER+    V  P +  T  GP++S K    VL Y E    EGA  +AGG        
Sbjct: 303 KRLTERLSTAVVGDPLDEATNFGPMVSEKQMKIVLDYIEKGENEGARLVAGGRRLN---- 358

Query: 364 RDNGAWVEPTVIAGLSDDARVVREEIFGPICHVTPFDSESEVIRRANDTRYGLAATIWTT 423
           RD G +++PTV A + DD  + REEIFGP+  V  F++E E I RAN T +GL+A ++T 
Sbjct: 359 RD-GFYLQPTVFADVKDDMIIAREEIFGPVMAVLDFETEEEAITRANSTEFGLSAGVFTR 417

Query: 424 NLSRAHRVSELMRVGISWVNTWFLRDLRTPFGGAGLSGIGREGGMHSLNFYSELTNVCVR 483
           +LSRAHRV   +  G  ++N++    +  PFGG  +SG+GRE    ++N YSE+ +V VR
Sbjct: 418 DLSRAHRVIAQLEAGSCFINSYNDAPVEAPFGGTKMSGVGRENSKAAINHYSEMKSVYVR 477

Query: 484 I-DKESP 489
           + D E+P
Sbjct: 478 MGDVEAP 484


Lambda     K      H
   0.320    0.136    0.417 

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: 590
Number of extensions: 30
Number of successful extensions: 5
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: 491
Length of database: 485
Length adjustment: 34
Effective length of query: 457
Effective length of database: 451
Effective search space:   206107
Effective search space used:   206107
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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