GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glpD in Shewanella sp. ANA-3

Align glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized)
to candidate 7026168 Shewana3_3310 FAD dependent oxidoreductase (RefSeq)

Query= CharProtDB::CH_091834
         (512 letters)



>lcl|FitnessBrowser__ANA3:7026168 Shewana3_3310 FAD dependent
           oxidoreductase (RefSeq)
          Length = 396

 Score =  189 bits (480), Expect = 2e-52
 Identities = 133/374 (35%), Positives = 191/374 (51%), Gaps = 20/374 (5%)

Query: 15  YDVAVVGGGINGVGIAADAAGRGLSVFLCEQHDLAQHTSSASSKLIHGGLRYLEHYEFRL 74
           YD+A++GGGI+GVGIA  AA  G S  L E+ ++   TS+ SSKLIHGGLRYLE  +  L
Sbjct: 9   YDIAIIGGGISGVGIAQYAAAAGYSTLLIEKGEIGGQTSANSSKLIHGGLRYLESGQVNL 68

Query: 75  VREALAEREVLLAKAPHIVKPLRFVLP-HRPHLRPAWMIRAGLFLY------DHLGKREK 127
           VR++L ER  LL  AP +VK + F +P ++   R  W IRAGL LY      D LG+   
Sbjct: 69  VRKSLQERRHLLDFAPSLVKAVPFYIPVYQDSQRNPWTIRAGLSLYALLSEFDPLGRFVS 128

Query: 128 LPASRGLRFTGSSPLKAE-IRRGFEYSDCAVDDARLVVLNAISAREHGAHVHTRTRCVSA 186
           +PA    RF G   LK + ++  F+Y D   DD  L    A SA   GAHV+     +  
Sbjct: 129 IPAVHWHRFNG---LKLQGLKAVFQYWDAQTDDKLLTQAVARSAEALGAHVYAEAEFLQL 185

Query: 187 RRSKGLWHLHLERSDGSLYSIRARALVNAAGPWVARFIQDDLKQKSPYGIRLIQGSHIIV 246
                   L   R  G +  I A+ ++NAAGPWV   I       +   +  +QG+H+++
Sbjct: 186 NHLSEQIDLSF-RLRGEVQQIDAKLVINAAGPWVNEVIAKVSPPLAGVELDWVQGAHLLL 244

Query: 247 PKLYEGEHAYILQNEDRRIVFAIPYLDRFTMIGTTDREYQGDPAKVAISEEETAYLLQVV 306
                    Y+    D+R++F +P+  +  +IGTT+ E     +   ++E E  YLL + 
Sbjct: 245 DLPAPDGILYLESCFDKRVIFVMPWYGQM-LIGTTETELTSLDSPPQVTESEINYLLGIY 303

Query: 307 NAHFKQQLAAAD----ILHSFAGVRPLCDDESDEPSAITRDYTLSLSAGNGEPPLLSVFG 362
             +F    +  +    I+ +F GVR L    S   SA  R     +      P LLS++G
Sbjct: 304 RHYFPLSASIDELKTKIVQTFCGVRVLPKQAS---SAFERPRDTLMQTSISHPRLLSLYG 360

Query: 363 GKLTTYRKLAESAL 376
           GKLTT+R  +   L
Sbjct: 361 GKLTTFRSTSAEVL 374


Lambda     K      H
   0.321    0.136    0.415 

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: 428
Number of extensions: 25
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: 512
Length of database: 396
Length adjustment: 33
Effective length of query: 479
Effective length of database: 363
Effective search space:   173877
Effective search space used:   173877
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: 51 (24.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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