GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Pseudomonas putida KT2440

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate PP_4422 PP_4422 succinate-semialdehyde dehydrogenase (NADP+)

Query= SwissProt::Q9I6M5
         (483 letters)



>FitnessBrowser__Putida:PP_4422
          Length = 490

 Score =  489 bits (1259), Expect = e-143
 Identities = 243/482 (50%), Positives = 326/482 (67%), Gaps = 2/482 (0%)

Query: 2   QLKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKAL 61
           +L+   L   +AY+DG WV  +   ++ V +PA  ++I  V     +    A+EAA +A 
Sbjct: 11  KLRRNDLLETRAYIDGRWVTGEG--SLDVTDPANDQVIAQVAHCDESWVDLAVEAASRAF 68

Query: 62  PAWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGE 121
             WR     +R   LR+W  LM ENQ+DLA +MT EQGKPL+E++GEI Y A+F+EWF  
Sbjct: 69  DGWRNTLPTQRGAVLRKWAALMRENQEDLAVIMTCEQGKPLSESRGEINYGANFVEWFAA 128

Query: 122 EAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKP 181
           E +R YG+TIP H P+ +++   QPIGVT AITPWNFPSAMITRKA  ALAAGC M++KP
Sbjct: 129 EGERCYGETIPSHLPNSQLVTKLQPIGVTVAITPWNFPSAMITRKAAAALAAGCPMIVKP 188

Query: 182 ASQTPYSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQL 241
           A +TP SALALA LAE AGIP GVF V+TG A ++   L +   VR  +FTGSTE+GR L
Sbjct: 189 APETPLSALALARLAEEAGIPGGVFQVLTGDAPKMSARLLAASAVRAFSFTGSTEVGRIL 248

Query: 242 MAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGV 301
           + + A  +KKVSLELGG+APFIVFDDA +  AVEG + +K+  +GQ C+ ANR+YV   +
Sbjct: 249 LRQSADTVKKVSLELGGHAPFIVFDDASIAEAVEGCIGAKFATSGQDCLGANRIYVHRNI 308

Query: 302 YDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPH 361
           Y  FV++   A  KL +G+GLE GV  GP+       K  E I++A+S GAK+  GG  +
Sbjct: 309 YGQFVEEFTKATEKLRVGHGLEEGVDIGPMTRVTVANKCREQISNALSLGAKLTCGGIDN 368

Query: 362 ALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYAR 421
            LG +F  PT+L DV     ++ +ETFGP+A +  F  E EV+  +N+TEFGLA+Y Y  
Sbjct: 369 HLGSSFVLPTVLADVTDKMDIAFEETFGPVAAILPFDSEDEVVTRANNTEFGLAAYVYTN 428

Query: 422 DLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLG 481
           DL R  RV+++LEYGMV +NT   +    PFGG K SGLGREGSK+G+ +Y+E+KY+C+G
Sbjct: 429 DLRRACRVSDRLEYGMVALNTPKFTGAPIPFGGWKQSGLGREGSKHGLAEYMELKYVCIG 488

Query: 482 GI 483
           G+
Sbjct: 489 GL 490


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: 616
Number of extensions: 16
Number of successful extensions: 3
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: 490
Length adjustment: 34
Effective length of query: 449
Effective length of database: 456
Effective search space:   204744
Effective search space used:   204744
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