GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Pseudomonas fluorescens FW300-N1B4

Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate Pf1N1B4_2417 Betaine aldehyde dehydrogenase (EC 1.2.1.8)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2417
          Length = 490

 Score =  322 bits (826), Expect = 1e-92
 Identities = 173/472 (36%), Positives = 275/472 (58%), Gaps = 9/472 (1%)

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

Query: 71  ERATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKG-EIVYAASFIEWFAEEAKRIYGD 129
           ER+  LRR  +++ E  D+LA L TL+ GK  +E +  +IV  A  +E++A     I G+
Sbjct: 67  ERSRILRRAVDILRERNDELAALETLDTGKAYSETRYVDIVTGADVLEYYAGLVPAIEGE 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 IVERVARIRVGNPEDENTNFGPLVSFAHMESVLGYIAKGKEEGARLLCGGDRLTDGEFAK 365

Query: 363 GNFFEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLG 422
           G F  PT+ T+  +   + +EE FGP+  +  ++ E +VI  +NDTEFGLA+    +DL 
Sbjct: 366 GAFVAPTVFTDCTDEMTIVREEIFGPVMSILTYETEEEVIRRANDTEFGLAAGVVTKDLN 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: 560
Number of extensions: 24
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 (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