GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Pseudomonas putida KT2440

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate PP_2694 PP_2694 Aldehyde dehydrogenase family protein

Query= SwissProt::P94391
         (515 letters)



>FitnessBrowser__Putida:PP_2694
          Length = 480

 Score =  261 bits (666), Expect = 5e-74
 Identities = 161/469 (34%), Positives = 240/469 (51%), Gaps = 14/469 (2%)

Query: 35  KDYPLVINGERVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRYTSP 94
           K Y   I+G+  E  A + + +P+D  +++G+  +AS E A QAIQAA  A   W  +  
Sbjct: 4   KTYNNYIDGQWCEGHATLGNYSPSDTGDLIGQYHQASAEQARQAIQAARAAQPLWAASGL 63

Query: 95  EERAAVLFRAAAKVRRRKHEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELAKG 154
           E R  VL     ++  RK E   LL +E GKP  E   +   +  F  YYA +++     
Sbjct: 64  ESRQQVLMAIGDELIARKEELGELLSREEGKPLAEGIGEVNRSGQFFHYYAAEVLRQMGE 123

Query: 155 KPVNSREGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATPVIA 214
              + R G   +    P GV  +I PWNF  A  A      +  GN VV KPA+  P  A
Sbjct: 124 TAASVRPGVDIEVHREPVGVVGIITPWNFPMATAAWKIAPALAFGNAVVFKPANLVPASA 183

Query: 215 AKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFERAAKVQ 274
               E++   GLP G  N V GSGA+VG+ L+   +   +TFTGS + G R+    A   
Sbjct: 184 WALTEIISRQGLPSGTFNLVMGSGADVGEALIQSAEIDALTFTGSLQTGRRVAVATA--- 240

Query: 275 PGQQHLKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYD 334
               +L R   EMG K+ +VV +DAD+ELA +     AF   GQKC+A SR +V + ++D
Sbjct: 241 ---GNLVRCQLEMGSKNALVVMDDADLELAVECALNGAFFGTGQKCTASSRLIVCDGIHD 297

Query: 335 QVLERV-IEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSGGTGDD 392
           + +E + + + + KV      A V +GPV D    ++ ++Y+++ + EG  L+ GG    
Sbjct: 298 RFVEALRLRMRQLKV-GHALEAGVQIGPVADARQLEQNLAYLQLAQAEGATLIEGGERLQ 356

Query: 393 --SKGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGAVIT 450
               GY+++P +F +     R+ +EE+FGP+    +V DF+EAL   N+TEYGLT  +IT
Sbjct: 357 LACDGYYMRPALFINSRNDMRINREEVFGPIACVIRVRDFEEALATLNDTEYGLTAGIIT 416

Query: 451 NNRKHIERAKQEFHVGNLYFNRNCTGAIVGYH-PFGGFKMSGTDSKAGG 498
            + +H    K+    G +  N    G    YH PFGG K S    +  G
Sbjct: 417 QSLRHASHFKRRAQTGCVMVNLPTAG--TDYHVPFGGRKASSFGPREQG 463


Lambda     K      H
   0.316    0.133    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: 530
Number of extensions: 25
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: 515
Length of database: 480
Length adjustment: 34
Effective length of query: 481
Effective length of database: 446
Effective search space:   214526
Effective search space used:   214526
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