GapMind for catabolism of small carbon sources

 

Aligments for a candidate for tdcB in Pseudomonas fluorescens FW300-N2E3

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate AO353_29000 AO353_29000 pyridoxal-5'-phosphate-dependent protein subunit beta

Query= BRENDA::Q96GA7
         (329 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_29000 AO353_29000
           pyridoxal-5'-phosphate-dependent protein subunit beta
          Length = 303

 Score =  223 bits (568), Expect = 5e-63
 Identities = 133/307 (43%), Positives = 184/307 (59%), Gaps = 14/307 (4%)

Query: 15  HVVTPLLESWALSQVAGMPVFLKCENVQPSGSFKIRGIGHFCQEMAKKGCRHLVCSSGGN 74
           H+ TPL+    LS      ++LK EN+QPSGSFK+RG+G  C   A++G + +VC SGGN
Sbjct: 3   HIRTPLILHPGLS-TPSRRIWLKLENLQPSGSFKLRGMGLLCTRAAEQGMKKVVCPSGGN 61

Query: 75  AGIAAAYAARKLGIPATIVLPESTSLQVVQRLQGEGAEVQLTGKVWDEANLRAQELAKRD 134
           AG A A AA  LG+ A+I++P +T      R+   GA+V + G+VWDEAN  A ELA   
Sbjct: 62  AGYATAVAAAALGLEASIIVPHTTPESTRARIAKTGAQVIVHGQVWDEANQLALELANAP 121

Query: 135 GWENVPPFDHPLIWKGHASLVQELKAVLRTPP--GALVLAVGGGGLLAGVVAGLLEVGWQ 192
             E VP FDHP +W+GH++++ E   +L+  P    +V +VGGGGLLAG++ GL      
Sbjct: 122 DTEYVPAFDHPTLWEGHSTMIDE---ILQDCPQVDTIVASVGGGGLLAGILTGLERHARL 178

Query: 193 HVPIIAMETHGAHCFNAAITAGKLVTLPDITSVAKSLGAKTVAARALECMQVCKIHSEVV 252
              IIA ET GA  F+AA+ AG  V L +I+S+A SLGA  VA   +E +Q       V+
Sbjct: 179 DCRIIACETEGAASFDAAVKAGHPVKLSEISSIASSLGALQVAQWPVEHIQHFPHTCVVL 238

Query: 253 EDTEAVSAVQQLLDDERMLVEPACGAALAAIYSGLLRRLQAEGCLPPSLTSVVVIVCGGN 312
            D EA+  V +  DD R LVEPACG +LA  Y       +A          VV+IVCGG 
Sbjct: 239 TDAEAIMGVVRYADDLRQLVEPACGVSLAVAYLDHPAIAEAH--------DVVIIVCGGI 290

Query: 313 NINSREL 319
           +I+++++
Sbjct: 291 SISAQKV 297


Lambda     K      H
   0.319    0.134    0.404 

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: 208
Number of extensions: 8
Number of successful extensions: 3
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: 329
Length of database: 303
Length adjustment: 27
Effective length of query: 302
Effective length of database: 276
Effective search space:    83352
Effective search space used:    83352
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 (21.8 bits)
S2: 48 (23.1 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 paper from 2022 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