GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocA in Pseudomonas simiae WCS417

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate GFF4637 PS417_23725 methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::P07275
         (575 letters)



>lcl|FitnessBrowser__WCS417:GFF4637 PS417_23725
           methylmalonate-semialdehyde dehydrogenase
          Length = 505

 Score =  130 bits (328), Expect = 1e-34
 Identities = 130/420 (30%), Positives = 193/420 (45%), Gaps = 42/420 (10%)

Query: 60  EVPLVINGERIYDNNERALFPQTNPANHQQVLANVTQATEKDVMNAVKAAKDAKKDWYNL 119
           +V L+INGE + ++         NPA  Q+VLA V  AT  +V  A+ AA  A + W   
Sbjct: 11  QVKLLINGEWV-ESKTTEWQDIVNPAT-QEVLAKVPFATADEVNAAIDAAHRAFQTWKLT 68

Query: 120 PFYDRSAIFLKAADLISTKYRYDMLAATMLG--QGKNVYQAEIDCITELSDFFRYYVKYA 177
           P   R  I LK   LI     +    A +L   QGK +  AE D    L       V++A
Sbjct: 69  PIGARMRIMLKLQALIR---EHSKRIAVVLSNEQGKTIADAEGDIFRGLE-----VVEHA 120

Query: 178 SDLYAQQPVESADGTWNKAEYRPLE---GFVYAVSPFNFTAIAANLIGAPALM-GNTVVW 233
             +   Q  E ++      +   L    G    ++PFNF A+    +   A+  GNT V 
Sbjct: 121 CSIGTLQMGEFSENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVL 180

Query: 234 KPSQTAALSNYLLMTVLEEAGLPKGVINFIPGDPVQVTDQVLADKDFGALHFTGSTNVFK 293
           KPS+   LS  LL+ +  EAG+P GV+N + G    V D +   KD  A+ F GST V  
Sbjct: 181 KPSEQDPLSTMLLVELALEAGVPAGVLNVVHGGK-DVVDALCTHKDIKAVSFVGSTAVGT 239

Query: 294 SLYGKIQSGVVEGKYRDYPRIIGETGGKNFHLVHPSANISHAVLSTIRGTFEFQGQKCSA 353
            +Y       + GK+    R+    G KN  +V P AN  H + + +   F   GQ+C A
Sbjct: 240 HVYD------LAGKHG--KRVQSMMGAKNHAVVLPDANREHTLNALVGAGFGAAGQRCMA 291

Query: 354 ASRLYLPESKSEEFLSDMFGILQSQNVVPMNTSASPISGGNLRGFMGPVIHEQSFDKLVK 413
            S + L    S+++L D+  + Q   V          +G      +GPVI +++  ++++
Sbjct: 292 TSVVVL-VGASKQWLPDLKALAQKLKV---------NAGSEAGTDVGPVISKRAKARILE 341

Query: 414 VIED-AKKDPELEILYGGQYDK----SQGWFVGPTVIKAKRPDHPYMSTEFFGPILTVYE 468
           +IE   K+  +LE+   G+  K     QG FVGPT+     P     + E FGP+L V E
Sbjct: 342 LIESGVKEGAKLEL--DGRDIKVPGFEQGNFVGPTLFSGVTPSMQIYTQEIFGPVLVVLE 399


Lambda     K      H
   0.318    0.135    0.401 

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: 605
Number of extensions: 31
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: 575
Length of database: 505
Length adjustment: 35
Effective length of query: 540
Effective length of database: 470
Effective search space:   253800
Effective search space used:   253800
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 (21.7 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