GapMind for catabolism of small carbon sources

 

Aligments for a candidate for putA in Pseudomonas fluorescens FW300-N2C3

Align delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 (characterized)
to candidate AO356_09270 AO356_09270 aldehyde dehydrogenase

Query= CharProtDB::CH_122352
         (572 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09270 AO356_09270 aldehyde
           dehydrogenase
          Length = 505

 Score =  158 bits (400), Expect = 4e-43
 Identities = 144/491 (29%), Positives = 223/491 (45%), Gaps = 35/491 (7%)

Query: 73  AGKEVKSSSSLTQSNPASHGPVATYSNATAKDVQAAIESALEARKS--WASTPFADRASV 130
           A K   S ++    NPA+   +   S   A+DV  A+  A EA +   W   P  +R +V
Sbjct: 28  AFKPAISGNTFATVNPATGELLTEVSACAAEDVDYAVSKAREAFEDGRWRLLPPGERKAV 87

Query: 131 FLKAADLISTKYRYDVMALTMHGQGKNAWQAEIDSAAELCDFFRFGVKYAEDLYAQQPVH 190
            LK A L+  K R+++  L     GK   + ++    +     R+  +  + LY     H
Sbjct: 88  LLKFAKLLE-KNRHELAVLESLDSGKPVRECQLVDVPDTIHTLRWHAEVIDKLYD----H 142

Query: 191 HAP---GVWNRVEYRPLEGFVYAISPFNFTAIGGNLAGAPALM-GNVVVWKPSPSAIASN 246
            AP        V   P+ G V  + P+NF  +       PAL  G  V+ KP+     + 
Sbjct: 143 TAPVGNDALTMVVREPI-GVVGCVLPWNFPLLMLAWKIGPALAAGCSVIVKPAEQTTLTT 201

Query: 247 WLVHQILLEAGLPKNVIQFVPGEAEEVTKTVLDHPDFAALHFTGSTNVFRNLYGQISTRV 306
             V ++  +AG+P  V+  V G  ++V + +  H D   + FTGST   R      +   
Sbjct: 202 LRVAELAFDAGVPAGVLNIVTGTGKDVGEPLGLHKDVDMVSFTGSTATGRRFLHYAADS- 260

Query: 307 AAGKYRSYPRIVGETGGKNFHLIHKSA-DIRNAAVQTVRGAFEYQGQKCSATSRVYVASS 365
                 +  R+V E GGKN  ++   A D+   A Q V GAF   G+ CSATSR+ V +S
Sbjct: 261 ------NLKRVVLECGGKNPAVVMDDAEDLDLVAEQVVNGAFWNMGENCSATSRLLVHAS 314

Query: 366 IADSFLEQVASEAKSLKVGPPSDFTNFCGPVIHEASFTKLAKVIDEAKNDPELELLAGGS 425
           + D  L+++ +  +  K+G P D  N  G ++    F K+   +D A +   LE + GG 
Sbjct: 315 VKDELLKRMGAYIREWKMGDPLDPQNRVGALVSSDHFEKVKSYLDYA-SASNLEAVYGG- 372

Query: 426 YDSSKGWYIQPTVYRTTNPDHPLLTRELFGPILVVYAYPDATEADFARIAQKIDATGEYG 485
            D+  G +IQPTV    + D  L   E+FGP+L V  +    EA    IA   D    YG
Sbjct: 373 -DTHDGAFIQPTVIDGVDRDSRLFQEEIFGPVLSVTTFNSICEA----IALANDT--HYG 425

Query: 486 LTGSVFAQD-REALAVANDVLRNAAGNFYINCKSTGAVVGQQPFGGARASGTNDKAGSGN 544
           L  SV+  + R A+ +A ++    AG   +NC   G      PFGG + SG   +  S  
Sbjct: 426 LAASVYTGNLRRAIKLAREI---RAGIVTVNCFGEGD--ASTPFGGYKESGFGGRDKSVF 480

Query: 545 LLSRFVSLRSI 555
              ++  +++I
Sbjct: 481 AHDQYTEIKTI 491


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: 641
Number of extensions: 34
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: 572
Length of database: 505
Length adjustment: 35
Effective length of query: 537
Effective length of database: 470
Effective search space:   252390
Effective search space used:   252390
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.

Links

Downloads

Related tools

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 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