GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gbuA in Phaeobacter inhibens BS107

Align Guanidinobutyrase; GBase; EC 3.5.3.7; D-arginase; EC 3.5.3.10 (uncharacterized)
to candidate GFF1960 PGA1_c19930 agmatinase SpeB

Query= curated2:Q8KZT5
         (353 letters)



>FitnessBrowser__Phaeo:GFF1960
          Length = 322

 Score =  214 bits (546), Expect = 2e-60
 Identities = 117/304 (38%), Positives = 171/304 (56%), Gaps = 10/304 (3%)

Query: 23  YAGAATYARLPRLDQVSKADVTVVGVPFDSGVSYRPGARFGANHVREASRLLRPYNP-AW 81
           + GA ++ R      ++  D+ V GVPFD  V+ RPG R G   +REAS L  P  P  W
Sbjct: 28  FGGATSFLRRKYTKDLTGVDIAVTGVPFDQAVTNRPGTRLGPRAIREASCLQSPDEPYGW 87

Query: 82  DVSPFENIQVADAGDMAVNPFNINEAIETIQQNALDLTANGSKLVTLGGDHTIALPLLRA 141
              P   + +AD GD+A +  ++      +  +   + A  +  V LGGDH I+ P+L+A
Sbjct: 88  PHKPLSTLAIADYGDLAFDHADVPAFPAALTDHIRGILATETASVVLGGDHYISFPILKA 147

Query: 142 AAERAGEPIAMLHFDAHLDTWDTYFGAEYTHGTPFRRAVEEGILDTEAISHVGTRGPLYG 201
            AE+ G PI++L FDAH DTW         HGT F +AV+ G++D +    VG R     
Sbjct: 148 YAEKHG-PISLLQFDAHTDTWPDDNMDRIDHGTMFYKAVKMGLVDPKTSVQVGIR----- 201

Query: 202 KKDLDDDHRFGFGIVTSADVYYQGVLETVAKIRDRIGNRPLYISVDIDVLDPAHAPGTGT 261
                +D   G  I+ +  V+  G +ET  +I+  +G+RP Y++ DID LDPA+APGTGT
Sbjct: 202 ---TTNDDTLGVNIIDAPTVHDIGPVETAKRIKAILGDRPTYLTFDIDCLDPAYAPGTGT 258

Query: 262 PEAGGITSRELLEIIRGFRGMNLVGADVVEVAPAYDHAEITGVAGSHVAYELVTLMADNA 321
           P  GG+TS +   I+R   G+N+ G DVVEV+P +D    T +AG+HVA E++ L+  N 
Sbjct: 259 PVWGGLTSAQASRILREIAGINIKGGDVVEVSPPFDTTGATAIAGAHVATEIICLLGWNM 318

Query: 322 VEGD 325
            + D
Sbjct: 319 RDND 322


Lambda     K      H
   0.318    0.137    0.402 

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: 364
Number of extensions: 21
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: 353
Length of database: 322
Length adjustment: 28
Effective length of query: 325
Effective length of database: 294
Effective search space:    95550
Effective search space used:    95550
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: 49 (23.5 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