GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo3_N2E3:AO353_29000
          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:

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