GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Phyllobacterium brassicacearum STM 196

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_106710819.1 CU102_RS09225 fructose-bisphosphate aldolase class I

Query= BRENDA::Q8L207
         (343 letters)



>NCBI__GCF_003010955.1:WP_106710819.1
          Length = 341

 Score =  477 bits (1227), Expect = e-139
 Identities = 244/341 (71%), Positives = 282/341 (82%), Gaps = 1/341 (0%)

Query: 1   MNERLEDIALTLVGAGKGILAADESTATIGKRFESIGVECTEDNRRAYREMLFTAKEAME 60
           M+ERLEDIA+ +V  GKG+LAADESTATI KRF++IG+E T D+RR YREMLF + EAM+
Sbjct: 1   MSERLEDIAIAMVANGKGLLAADESTATIKKRFDTIGLESTADSRRDYREMLFRSDEAMK 60

Query: 61  SAISGVILFDETLRQKASTGQMLTDLIRDAGAVPGIKVDTGAKPLAAFPQETITEGLDGL 120
           + ISGVIL+DET+RQ A+ G     +++ AG +PGIKVD GAKPLA +P ETITEGLDGL
Sbjct: 61  NNISGVILYDETIRQSANDGTPFVQIMKAAGCIPGIKVDAGAKPLAGYPGETITEGLDGL 120

Query: 121 RERLKDYYTLGARFAKWRAVIAIDAQTLPTRGAISQNAQALARYAALCQEAGLVPIVEPE 180
           RERL++YY LGARFAKWR VI I A+ +PT GA+ QNAQALARYAALCQEAG+VPIVEPE
Sbjct: 121 RERLQEYYGLGARFAKWRGVIGI-AEGIPTWGAVKQNAQALARYAALCQEAGIVPIVEPE 179

Query: 181 VLMDGPSRQHSITRCFEVTKVVLHTVFKELFEARVLFEGMILKPNMVIDGKDARIASVEE 240
           VLMDG    HSI RC+EVT+ VL TVF EL++ARV  EGMILKPNMVIDGK+AR ASVE+
Sbjct: 180 VLMDGKPATHSIERCYEVTEWVLKTVFDELYDARVKLEGMILKPNMVIDGKNARKASVEQ 239

Query: 241 VAEKTVHVLKQTVPAAVPGIAFLSGGQTDEEATAHLSAMNALGALPWKLTFSYGRALQAA 300
           VAE+TV VLK TVPAAV GIAFLSGGQ+DEEATAHLSAMNA    PWKLTFSYGRALQAA
Sbjct: 240 VAEQTVRVLKSTVPAAVAGIAFLSGGQSDEEATAHLSAMNANFTTPWKLTFSYGRALQAA 299

Query: 301 ALKAWAGKNENIVVAQKAFCHRARMNHLAALGQWTKDQEKS 341
           A+ AW GK EN+   Q+AF HRA+MN LAA G W KD EK+
Sbjct: 300 AINAWNGKPENVAAGQRAFTHRAKMNGLAATGGWKKDLEKA 340


Lambda     K      H
   0.319    0.132    0.378 

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: 391
Number of extensions: 12
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: 343
Length of database: 341
Length adjustment: 29
Effective length of query: 314
Effective length of database: 312
Effective search space:    97968
Effective search space used:    97968
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: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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