GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Pseudomonas fluorescens FW300-N1B4

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate Pf1N1B4_1229 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)

Query= BRENDA::P07275
         (575 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1229
          Length = 505

 Score =  129 bits (323), Expect = 4e-34
 Identities = 129/420 (30%), Positives = 196/420 (46%), Gaps = 42/420 (10%)

Query: 60  EVPLVINGERIYDNNERALFPQTNPANHQQVLANVTQATEKDVMNAVKAAKDAKKDWYNL 119
           +V L+I+GE + ++         NPA  QQVLA V  AT  +V  A+ AA  A + W   
Sbjct: 11  KVKLLIDGEWV-ESQTTEWHDIVNPAT-QQVLAKVPFATAAEVDAAISAAHRAFQTWKLT 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 A+      +   L    G    ++PFNF A+    +   A+  GNT V 
Sbjct: 121 CSIGSLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVL 180

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

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

Query: 354 ASRLYLPESKSEEFLSDMFGILQSQNVVPMNTSASPISGGNLRGFMGPVIHEQSFDKLVK 413
            S + L    ++++L D+  + Q   V   N  + P +       +GPVI +++  +++ 
Sbjct: 292 TSVVVL-VGAAKQWLPDLKALAQKLKV---NAGSEPGTD------VGPVISKRAKARILD 341

Query: 414 VIEDA-KKDPELEI----LYGGQYDKSQGWFVGPTVIKAKRPDHPYMSTEFFGPILTVYE 468
           +IE   K+  +LE+    +    Y+K  G FVGPT+     P+    + E FGP+L V E
Sbjct: 342 LIESGIKEGAKLELDGRDISVPGYEK--GNFVGPTLFSGVTPEMQIYTQEIFGPVLVVLE 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: 602
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 (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