GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Paraburkholderia bryophila 376MFSha3.1

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate H281DRAFT_03178 H281DRAFT_03178 succinate semialdehyde dehydrogenase

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



>FitnessBrowser__Burk376:H281DRAFT_03178
          Length = 486

 Score =  202 bits (514), Expect = 2e-56
 Identities = 153/463 (33%), Positives = 220/463 (47%), Gaps = 12/463 (2%)

Query: 5   YIAGEWL-AGGGEAFESLNPVTQQVLWSGVGATAGQVESAVQAARQAFPDWARRTLEERI 63
           Y+AGEW  A  G  FE +NP T +V+ +       +   A+ AA  A+P W   T ++R 
Sbjct: 17  YLAGEWQGADDGSTFEVVNPATGEVVATVPRMGTAETRRAIDAANAAWPAWRASTAKQRA 76

Query: 64  SVLEAFAAALKNHADELAHTIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK-SG 122
            +L  +   +  +AD+LA  +  E GKPL EA  E+    + +    +  +   G+    
Sbjct: 77  VILRKWHDLMLENADDLALILTTEQGKPLAEAKGEIQYAASFLEWFAEEGKRLNGDTIPT 136

Query: 123 PLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAELTV 182
           P  D   V+  +P GV A   P+NFP  +    + PAL AG  ++ KP+E TP  A    
Sbjct: 137 PANDKRIVVTKEPVGVCAAITPWNFPAAMITRKVGPALAAGCPIIVKPAEATPLSALALA 196

Query: 183 KCWIEAGLPAGVLNLLQG-ARETGIALAANPGIDGLFFTGSSRTGNHLHQQFAGRPDKIL 241
                AG+P GV N++ G  +  G  +  NP +  L FTGS+  G  L  Q A    K+ 
Sbjct: 197 VLAERAGVPRGVFNVVTGEPKAIGAEMTGNPIVRKLSFTGSTPVGRLLMAQCAPTVKKV- 255

Query: 242 ALEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDSLLARLVA 301
           +LE+GGN P +V   ADLDAAV   I S + ++GQ C C  R  V    + D+  A+L A
Sbjct: 256 SLELGGNAPFIVFDDADLDAAVAGAIASKYRNSGQTCVCTNRFYVHDKVY-DAFAAKLRA 314

Query: 302 VSSTLSVGAFDQQPAPFMGSVVSLGAAKALMDAQEHLLANGAVALLEMTQPQAQSALLTP 361
               L+VG    +     G +++  A   +    E  LA GA  +    +         P
Sbjct: 315 AVEQLTVGR-GTEAGVTQGPLINEAAVLKVESHIEDALAKGARVVTGGKRHALGHGFFEP 373

Query: 362 GIL-DVSAVADRPDEELFGPLLQVIRYADFEAAIAEANDTAYGLAAGLLSDSEARYQQFW 420
            IL DV+       +E FGPL  + R++  E  IA ANDT +GLA+   S    R  +  
Sbjct: 374 TILADVTPDMKVARDETFGPLAPLFRFSSDEEVIALANDTEFGLASYFYSRDIGRVWRVA 433

Query: 421 LESRAGIVNWNKQLTGAASS--APFGGVGASGNHRASAYYAAD 461
                G+V  N   TG  S+  APFGGV  SG  R  ++Y  D
Sbjct: 434 EALEYGMVGIN---TGLISNEVAPFGGVKQSGLGREGSHYGID 473


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: 514
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: 488
Length of database: 486
Length adjustment: 34
Effective length of query: 454
Effective length of database: 452
Effective search space:   205208
Effective search space used:   205208
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