GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Pseudomonas fluorescens FW300-N2C3

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate AO356_29070 AO356_29070 succinate-semialdehyde dehydrogenase

Query= SwissProt::Q9I6M5
         (483 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_29070
          Length = 489

 Score =  602 bits (1552), Expect = e-177
 Identities = 290/483 (60%), Positives = 381/483 (78%), Gaps = 3/483 (0%)

Query: 3   LKDAKLFRQQAYVDGAWV-DADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKAL 61
           LKD  L+R  AY+ G W+ +  NGQ   + NP    ++  +P+ G AE R AI+AA +A 
Sbjct: 5   LKDPTLWRTGAYIAGEWLTETPNGQ-YTLRNPVDQSVLAELPRCGEAEVRHAIDAAHEAF 63

Query: 62  PAWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGE 121
             WR LTAK R   LRRW++LM+E+++D+A L+T+E+GKPL EA+GE+ YAASF+ WFGE
Sbjct: 64  GPWRRLTAKRRGEVLRRWYELMVEHREDIATLITLEEGKPLEEARGEVDYAASFVRWFGE 123

Query: 122 EAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKP 181
           EA R+ GD IPG +  +RI+V+++PIGV AAITPWNFP+AMITRKA PALAAGCTMV+KP
Sbjct: 124 EATRVRGDLIPGVKDTQRIVVLREPIGVCAAITPWNFPAAMITRKAAPALAAGCTMVVKP 183

Query: 182 ASQTPYSALALAELAERAGIPKGVFSVVTGS-AGEVGGELTSNPIVRKLTFTGSTEIGRQ 240
           ASQTP +ALALAELA RAG+P GVFSV+TG+   ++ GELT+NP+VRKLTFTGSTE+GR 
Sbjct: 184 ASQTPLTALALAELALRAGVPAGVFSVITGNDTRDIAGELTANPLVRKLTFTGSTEVGRL 243

Query: 241 LMAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDG 300
           L+A+ AQ +KK S+ELGGNAPFIVFDDADLDAA +G +++K+RN GQ+C+ ANR+ VQ G
Sbjct: 244 LLAQAAQTVKKCSMELGGNAPFIVFDDADLDAAADGVMLAKFRNGGQSCIGANRVLVQSG 303

Query: 301 VYDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKP 360
           VYDA  +++   +A+L +GNGLE GV  GPLID  AV K +  + DA+++GA+++SGGKP
Sbjct: 304 VYDALAERIVERMARLKVGNGLEPGVQVGPLIDDAAVRKSQALVDDALAQGARLLSGGKP 363

Query: 361 HALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYA 420
           HALGG FF+PT+L DV     V+++E FGP+ P+ RF  + E IAM+ND+EFGLA+Y ++
Sbjct: 364 HALGGCFFQPTLLADVTHGMRVAREEIFGPVMPLVRFDRDDEAIAMANDSEFGLAAYLFS 423

Query: 421 RDLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 480
           RD AR++R A ++E GMVGIN GLISNEVAPFGG+K SGLGREGS  GI+++LE+KYLC 
Sbjct: 424 RDAARIWRNAARIESGMVGINCGLISNEVAPFGGVKQSGLGREGSHLGIDEFLEVKYLCW 483

Query: 481 GGI 483
            G+
Sbjct: 484 DGL 486


Lambda     K      H
   0.317    0.135    0.391 

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: 652
Number of extensions: 18
Number of successful extensions: 2
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: 483
Length of database: 489
Length adjustment: 34
Effective length of query: 449
Effective length of database: 455
Effective search space:   204295
Effective search space used:   204295
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