GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mmsA in Pseudomonas fluorescens FW300-N1B4

Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate Pf1N1B4_4931 Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20); Succinate-semialdehyde dehydrogenase [NADP+] (EC 1.2.1.79)

Query= reanno::psRCH2:GFF2388
         (503 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4931
           Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20);
           Succinate-semialdehyde dehydrogenase [NADP+] (EC
           1.2.1.79)
          Length = 485

 Score =  231 bits (588), Expect = 6e-65
 Identities = 153/456 (33%), Positives = 241/456 (52%), Gaps = 10/456 (2%)

Query: 14  IDGEFIESTTQDWRDVVNPATQEVLARVPFATAEEIDRAVASGQKAFKTWRKTPIGARAR 73
           +DG++I +      DV++PA+ ++LARVP     +  RA+ + ++A+  WR  P   RA 
Sbjct: 18  VDGQWIGADNAATLDVIDPASGQLLARVPAMQGAQTRRAIEAAERAWPAWRARPAAERAA 77

Query: 74  IFLKYQQLIRENMKELAAILTAEQGKTLADAEGDVFRGLEVVEHAAGIGNLQLGELANNV 133
           +  ++ Q + +N+ +LA I+T EQGK L +A+G++  G   V+  A       GE     
Sbjct: 78  LLERWYQAMIDNLDDLALIMTCEQGKPLNEAKGEIRYGAGFVKWFAEEARRVYGETMPAP 137

Query: 134 AAGVDTYTLLQPLGVCAGITPFNFP-AMIPLWMFPMAIATGNTFVLKPSEQDPMVTMRLC 192
           +      TL QP+GVCA ITP+NFP AMI     P A+A G   ++KPS+  P+  + L 
Sbjct: 138 SGDRRLLTLKQPVGVCAAITPWNFPNAMITRKCAP-ALAAGCPIIVKPSDLTPLSALALA 196

Query: 193 ELALEAGVPPGVLNVVHGGP-DVVNAICDHPDIKAVSFVGSTKVGTHVYNRASQAGKRVQ 251
            LA   G+P GV NV+ G P  +   +  +P ++ +SF GST VG  +  ++++  KR+ 
Sbjct: 197 VLAERVGIPAGVFNVLTGMPAGIGEELTGNPTVRKISFTGSTAVGRLLMRQSAEHIKRLS 256

Query: 252 CMMGAKNHAIVLPDAHKEQTLNNLAGAAFGAAGQRCM-ALSVVVLVGEAQAWIPDLVAKA 310
             +G     IV  DA  EQ +  +  + F  AGQ C+ A  ++V  G  + +   LV + 
Sbjct: 257 LELGGNAPFIVFDDADLEQAVAGIMLSKFRNAGQTCVCANRILVQDGIYERFAQRLVEEV 316

Query: 311 QTLKVNAGVEAGTDVGPLVSCAALDRVSGLIERGVREGAKLELDGRNPSVSGYENGNFVG 370
             LKV  G++A   +GPL++ AA+ +++  I+  + +GA+L L G  P      +  FV 
Sbjct: 317 GKLKVGNGLDADVTIGPLINPAAVSKIARHIDDALSQGARL-LCGGIPE----GDSQFVQ 371

Query: 371 PTIFSGVTREMSVYQEEIFGPVLCVMAAATMDEAIELINANPNGNGTAIFTRSGAAARHF 430
           PT+       M +  EE FGPV  +M      EA+ L NA P G G   FT+    +  F
Sbjct: 372 PTVLGDTHAGMLLANEETFGPVAPLMRFTDEAEALALANATPYGLGAYYFTQDLRRSWRF 431

Query: 431 QEEIDVGQVGINVPIPVPVPMFSFTGSRASKLGDLG 466
            E ++ G VG+N  I + + +  F G + S LG  G
Sbjct: 432 GEALEFGMVGLNTGI-ISMEVAPFGGIKQSGLGREG 466


Lambda     K      H
   0.318    0.134    0.394 

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: 547
Number of extensions: 22
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: 503
Length of database: 485
Length adjustment: 34
Effective length of query: 469
Effective length of database: 451
Effective search space:   211519
Effective search space used:   211519
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, 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