GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Putida:PP_2694 PP_2694 Aldehyde dehydrogenase
           family protein
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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