GapMind for catabolism of small carbon sources

 

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

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate WP_085635633.1 MGEO_RS04980 NAD-dependent succinate-semialdehyde dehydrogenase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1974
         (488 letters)



>NCBI__GCF_002115805.1:WP_085635633.1
          Length = 476

 Score =  190 bits (483), Expect = 8e-53
 Identities = 143/461 (31%), Positives = 218/461 (47%), Gaps = 13/461 (2%)

Query: 4   LYIAGEWLAGGG-EAFESLNPVTQQVLWSGVGATAGQVESAVQAARQAFPDWARRTLEER 62
           LYI G W++G   E F+ LNP T++VL S   A     ++A+ AA  A  +WA RT  ER
Sbjct: 6   LYINGTWVSGASKERFDVLNPATEEVLASVASAEIADADAALDAAEAAMAEWAARTPRER 65

Query: 63  ISVLEAFAAALKNHADELAHTIGEETGKPLWEAATEVTSMVNKIA-ISVQSYRERTGEKS 121
             VL      +    ++ A  I  E GK   +A  E T         + ++ R       
Sbjct: 66  SEVLRKAWELMTVRLEDFAKLITLENGKARTDAMGEATYAAEFFRWFAEEAVRADGLITH 125

Query: 122 GPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAELT 181
            P   A  +++HKP G+  +  P+N+P  +    I PAL AG +V+ KP+  TP      
Sbjct: 126 APASGARIMVQHKPAGLAVLVTPWNYPAAMGTRKIAPALAAGCAVIIKPASETPLTMLAL 185

Query: 182 VKCWIEAGLPAGVLNLLQGARETGIA--LAANPGIDGLFFTGSSRTGNHLHQQFAGRPDK 239
           +    EAG+P G++N+L   R   +   +  +P +  + FTGS+  G  L    A   D+
Sbjct: 186 MPLLEEAGVPPGLVNVLPSKRTGALVDHMLHDPRVRVVSFTGSTGVGRKLLHSAA---DQ 242

Query: 240 IL--ALEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDSLLA 297
           +L  A+E+GGN P+VV + AD+D A+   + +   + G+ CT A R+ V + A  ++   
Sbjct: 243 VLKPAMELGGNAPVVVFEDADMDTAIEGTMLAKMRNLGEACTAANRIYVHE-AIAETFTK 301

Query: 298 RLVAVSSTLSVGAFDQQPAPFMGSVVSLGAAKALMDAQEHLLANGAVALLEMTQPQAQSA 357
           RL    S L VG     P   +G +V+      + +     +A GA+     T P+    
Sbjct: 302 RLTEKMSALKVGD-GIDPTVDVGPLVNAETRDKVAEFVADAVAKGAIIECGGTTPEGPGF 360

Query: 358 LLTPGIL-DVSAVADRPDEELFGPLLQVIRYADFEAAIAEANDTAYGLAAGLLSDSEARY 416
              P +L +V   AD   +E+FGP+  +  + D E  I  ANDT YGL A + S    R 
Sbjct: 361 YYPPTVLSNVPETADCVHDEIFGPVAAIQTFRDQEEVIRRANDTEYGLVAYVFSGDMKRA 420

Query: 417 QQFWLESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAY 457
            Q       G+V  N+ L  +  +APFGG   SG  R   +
Sbjct: 421 LQVCERLDYGMVGLNRGLV-SDPAAPFGGTKQSGLGREGGH 460


Lambda     K      H
   0.316    0.132    0.388 

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: 490
Number of extensions: 30
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: 488
Length of database: 476
Length adjustment: 34
Effective length of query: 454
Effective length of database: 442
Effective search space:   200668
Effective search space used:   200668
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