GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davD in Pseudomonas fluorescens FW300-N2E3

Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate AO353_07805 AO353_07805 betaine-aldehyde dehydrogenase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_495
         (480 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_07805 AO353_07805
           betaine-aldehyde dehydrogenase
          Length = 490

 Score =  327 bits (837), Expect = 7e-94
 Identities = 176/472 (37%), Positives = 276/472 (58%), Gaps = 9/472 (1%)

Query: 11  QQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAK 70
           Q+ +IDG + DA    T +  NPA GE+L TV +   A+  RA+ +A+K    W A+TA 
Sbjct: 7   QKLYIDGGYSDASGDATFEAINPANGEVLATVQRATFADVERAVVSAEKGQKIWAAMTAM 66

Query: 71  ERATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKG-EIVYAASFIEWFAEEAKRIYGD 129
           ER+  LRR  E++ E  D+LA L TL+ GK  +E +  +IV  A  +E++A     I G+
Sbjct: 67  ERSRILRRAVEILRERNDELAALETLDTGKAYSETRYVDIVTGADVLEYYAGLVPAIEGE 126

Query: 130 VIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSA 189
            IP  +    +   ++P+G+ A I  WN+P  +   K+ PALAAG  M+ KP+  T  + 
Sbjct: 127 QIP-LRTTSFVYTRREPLGIVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTSLTT 185

Query: 190 FALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLM-SECAKD 248
             LAE+   AG+PAGVF+V++GS  ++G+ LT +P + K+SFTG T+ G+++M S     
Sbjct: 186 LKLAEIYTEAGLPAGVFNVLTGSGREVGTWLTEHPRIEKISFTGGTDTGKKVMASASGSS 245

Query: 249 IKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAEK 308
           +K V++ELGG +P I+FDDADLD+A + A+++ + ++GQ C    R+++   +  AF  K
Sbjct: 246 LKDVTMELGGKSPLIIFDDADLDRAADTAMMANFYSSGQVCTNGTRVFVPSHLKAAFEAK 305

Query: 309 LKVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGKPM------E 362
           +   VA++++GN  +  T  GPL+    +  V  +IA    +GA +L GG+ +      +
Sbjct: 306 IVERVARIRVGNPEDENTNFGPLVSFAHMESVLGYIAKGKEEGARLLCGGERLTEGEFAK 365

Query: 363 GNFFEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLG 422
           G F  PT+ T+  +   + +EE FGP+  +  ++ E +VI  +NDTEFGLA+    RDL 
Sbjct: 366 GAFVAPTVFTDCTDEMTIVREEIFGPVMSILTYETEEEVIRRANDTEFGLAAGVVTRDLN 425

Query: 423 RVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474
           R  RV   LE G+  +N    S+   P GG K SG+GRE     + ++  IK
Sbjct: 426 RAHRVIHQLEAGICWINAWGESDAKMPVGGYKQSGVGRENGISSLNNFTRIK 477


Lambda     K      H
   0.317    0.135    0.390 

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: 573
Number of extensions: 23
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: 480
Length of database: 490
Length adjustment: 34
Effective length of query: 446
Effective length of database: 456
Effective search space:   203376
Effective search space used:   203376
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 (21.7 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 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, 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