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

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources