GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Pseudomonas fluorescens GW456-L13

Align delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 (characterized)
to candidate PfGW456L13_1397 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= CharProtDB::CH_122352
         (572 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1397
          Length = 496

 Score =  162 bits (411), Expect = 2e-44
 Identities = 145/472 (30%), Positives = 228/472 (48%), Gaps = 37/472 (7%)

Query: 75  KEVKSSSSLTQSNPASHGPVATYSNATAKDVQAAIESALEARKS--WASTPFADRASVFL 132
           +  +S  +    NPA+   +A  +    +DV AA+ +A +  ++  WA+    +R  V L
Sbjct: 27  RPAQSGQTFAAINPATSQCLANVAACGEEDVNAAVHNARQVFEAGTWAARSPTERKQVLL 86

Query: 133 KAADLISTKYRYDVMALTMHGQGK---NAWQAEIDSAAELCDFFRFGVKYAEDLYAQQPV 189
           + ADLI  + R ++  L     GK   +A+  ++  AA +   FR+  +  + LY Q   
Sbjct: 87  RLADLI-LENREELALLDSLNMGKPVADAYNIDVPGAAGV---FRWYAESLDKLYDQV-- 140

Query: 190 HHAPGVWNRVEY--RPLEGFVYAISPFNFTAIGGNLAGAPALM-GNVVVWKPSPSAIASN 246
             AP   N +    R   G V A+ P+NF         APAL  GN V+ KP+  +  S 
Sbjct: 141 --APSAQNVLATITREALGVVAAVVPWNFPLDMAAWKLAPALAAGNSVILKPAEQSPFSA 198

Query: 247 WLVHQILLEAGLPKNVIQFVPGEAEEVTKTVLDHPDFAALHFTGSTNVFRNLYGQISTRV 306
             + ++ LEAG+P  V+  +PG  E+  K +  HPD   L FTGST V +  + Q S + 
Sbjct: 199 LRLAELALEAGVPAGVLNVLPGLGEQTGKALGLHPDVDCLVFTGSTEVGK-YFMQYSAQ- 256

Query: 307 AAGKYRSYPRIVGETGGKNFHLIHKSA-DIRNAAVQTVRGAFEYQGQKCSATSRVYVASS 365
                 +  ++  E GGK+ +L+     D+  AA +   G F  QG+ CSA SR+ V  S
Sbjct: 257 -----SNLKQVWLECGGKSANLVFADCQDLDLAAEKAAFGIFFNQGEVCSANSRLLVQRS 311

Query: 366 IADSFLEQVASEAKSLKVGPPSDFTNFCGPVIHEASFTKLAKVIDEAKNDPELELLAG-G 424
           I D F+E++ ++A+    G P D ++  G ++      ++ K I +A+      +  G  
Sbjct: 312 IHDEFVERLKAQAERWLPGDPLDPSSAAGAIVDSRQTARIMKFIQQAEQQGATRICGGRQ 371

Query: 425 SYDSSKGWYIQPTVYRTTNPDHPLLTRELFGPILVVYAYPDATEADFARIAQKIDATGEY 484
           S  +    +IQPT++    PD PL   E+FGP+L V A+ D  EA   ++A        Y
Sbjct: 372 SIINGSDNFIQPTIFTGVTPDMPLFRDEVFGPVLAVTAFDD--EAHALQLAN----DSVY 425

Query: 485 GLTGSVFAQDREALAVANDVLRN-AAGNFYINCKSTGAVVGQQPFGGARASG 535
           GL  S++  D   L  A+ V R   AG   +N  S  A+    PFGG + SG
Sbjct: 426 GLAASLWTDD---LNRAHRVARQLRAGTVSVN--SVDALDVTVPFGGGKQSG 472


Lambda     K      H
   0.316    0.130    0.379 

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: 587
Number of extensions: 33
Number of successful extensions: 5
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: 572
Length of database: 496
Length adjustment: 35
Effective length of query: 537
Effective length of database: 461
Effective search space:   247557
Effective search space used:   247557
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 (21.6 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