GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Pseudomonas stutzeri RCH2

Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate GFF2584 Psest_2634 glycine betaine aldehyde dehydrogenase

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



>FitnessBrowser__psRCH2:GFF2584
          Length = 490

 Score =  332 bits (851), Expect = 2e-95
 Identities = 182/473 (38%), Positives = 281/473 (59%), Gaps = 9/473 (1%)

Query: 10  RQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTA 69
           RQQ +I G +VDA + +T +  NPA GE+L  V + GAA+  RA+E+A++    W ALT 
Sbjct: 6   RQQLYIHGGYVDASSNETFESINPANGEVLAQVAEAGAADLERAVESAEQGQRIWAALTG 65

Query: 70  KERATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKG-EIVYAASFIEWFAEEAKRIYG 128
            ERA  +RR  +L+ E  D+LA L TL+ GKPL+E +  +IV  A  +E++A  A  I G
Sbjct: 66  IERARIMRRAVDLLRERNDELALLETLDTGKPLSETRSVDIVTGADVLEYYAGLAPAIEG 125

Query: 129 DVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFS 188
           + IP  +    +   ++P+GV A I  WN+P  +   KA PALAAG  M+ KP+  T  S
Sbjct: 126 EQIP-LRDSSFVYTRREPLGVVAGIGAWNYPIQIALWKAAPALAAGNAMIFKPSEVTSLS 184

Query: 189 AFALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECA-K 247
           A  LAE+   AG+P GVF+V++GS   +G+ +T +P + K+SFTG    G+++M+  A  
Sbjct: 185 ALKLAEIFSEAGLPDGVFNVLTGSGAGVGALITEHPRIAKVSFTGGVATGKKVMASAASS 244

Query: 248 DIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAE 307
            +K V++ELGG +P I+ +DADLD+A + A+++ + ++GQ C    R+++  G+  AF  
Sbjct: 245 SLKDVTMELGGKSPLIICEDADLDRAADIAVMANFFSSGQVCTNGTRVFVPAGLKAAFEA 304

Query: 308 KLKVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGKPM------ 361
           KL   V ++++G+  +  T  GPL+    +  V ++IA   + GA +L GG+ +      
Sbjct: 305 KLLERVQRIRLGDPQQEETNFGPLVSFAHMNNVLDYIAKGKAAGARLLCGGERVTEGEYA 364

Query: 362 EGNFFEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDL 421
           +G F  PTI ++  ++ A+  EE FGP+  L  ++DE +VI  +NDTE+GLA+     DL
Sbjct: 365 KGAFVAPTIFSDCSDDMAIVCEEIFGPVLSLLEYQDEDEVIRRANDTEYGLAAGVVTADL 424

Query: 422 GRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474
            R  R+   LE G+  +NT   S    P GG K SG+GRE     +  Y  +K
Sbjct: 425 ARAHRIIHRLEAGICWINTWGESPAQMPVGGYKQSGIGRENGIASLAHYTRVK 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: 554
Number of extensions: 25
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