GapMind for catabolism of small carbon sources

 

Aligments for a candidate for kbl in Pseudomonas stutzeri RCH2

Align 8-amino-7-oxononanoate synthase/2-amino-3-ketobutyrate coenzyme A ligase; AONS/AKB ligase; 7-keto-8-amino-pelargonic acid synthase; 7-KAP synthase; KAPA synthase; 8-amino-7-ketopelargonate synthase; Alpha-oxoamine synthase; Glycine acetyltransferase; EC 2.3.1.29; EC 2.3.1.47 (characterized)
to candidate GFF411 Psest_0412 8-amino-7-oxononanoate synthase

Query= SwissProt::Q5SHZ8
         (395 letters)



>lcl|FitnessBrowser__psRCH2:GFF411 Psest_0412 8-amino-7-oxononanoate
           synthase
          Length = 392

 Score =  266 bits (679), Expect = 1e-75
 Identities = 161/383 (42%), Positives = 210/383 (54%), Gaps = 6/383 (1%)

Query: 1   MSLDLRARVREELERLKREGLYISPKVLEAPQEPVTRVEGREVVNLASNNYLGFANHPYL 60
           M+ DL +R+ E     +   LY    +LE PQ+P   V+G  ++   SN+YLG A+HP +
Sbjct: 1   MTFDLASRLAER----RAAHLYRQRPLLETPQQPEVMVDGERLLAFCSNDYLGLASHPEV 56

Query: 61  KEKARQYLEKWGAGSGAVRTIAGTFTYHVELEEALARFKGTESALVLQSGFTANQGVLGA 120
               +Q   KWG G GA   + G  T H +LEEALA F G   AL+  +G+ AN   + A
Sbjct: 57  IAAMQQGAAKWGVGGGASHLVIGHSTPHHQLEEALADFTGRPRALLFSTGYMANLAAVTA 116

Query: 121 LLKEGDVVFSDELNHASIIDGLRLTKATRLVFRHADVAHLEELLKAHDTDGLKLIVTDGV 180
           L+ +GD V  D LNHAS++D   L+ A    + H D   L + L      G  L+VTDGV
Sbjct: 117 LVGQGDTVLEDRLNHASLLDAGLLSGARFSRYLHNDAEILAKRLDK--AGGNTLVVTDGV 174

Query: 181 FSMDGDIAPLDKIVPLAKKYKAVVYVDDAHGSGVLGEKGKGTVHHFGFHQDPDVVQVATL 240
           FSMDGD+A L  I   AK   A V VDDAHG G LG  G G V  FG   D   V V TL
Sbjct: 175 FSMDGDLADLPAICATAKPRGAWVMVDDAHGFGPLGATGGGIVEQFGLGIDDVPVLVGTL 234

Query: 241 SKAWAGIGGYAAGARELKDLLINKARPFLFSTSHPPAVVGALLGALELIEKEPERVERLW 300
            KA+   G + AG+ EL + LI  ARP++++TS PPAV  A L +LEL+  E  R E L 
Sbjct: 235 GKAFGTAGAFVAGSEELIETLIQFARPYIYTTSQPPAVACATLKSLELLSSEGWRREHLN 294

Query: 301 ENTRYFKRELARLGYDTLGSQTPITPVLFGEAPLAFEASRLLLEEGVFAVGIGFPTVPRG 360
                F+    ++G   + S TPI PVL G +  A   S LL E G+    I  PTVP G
Sbjct: 295 RLVARFREGAQQIGLTLMDSPTPIQPVLVGSSERALRLSALLRERGILVGAIRPPTVPAG 354

Query: 361 KARIRNIVTAAHTKEMLDKALEA 383
            AR+R   TA+H+   L++ LEA
Sbjct: 355 SARLRITFTASHSDAQLERLLEA 377


Lambda     K      H
   0.319    0.137    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: 350
Number of extensions: 18
Number of successful extensions: 2
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: 395
Length of database: 392
Length adjustment: 31
Effective length of query: 364
Effective length of database: 361
Effective search space:   131404
Effective search space used:   131404
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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 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