GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Pontibacter ramchanderi LP43

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_101443621.1 BD749_RS04795 glucose 1-dehydrogenase

Query= reanno::pseudo1_N1B4:Pf1N1B4_412
         (272 letters)



>NCBI__GCF_002846395.1:WP_101443621.1
          Length = 247

 Score =  143 bits (360), Expect = 4e-39
 Identities = 84/244 (34%), Positives = 135/244 (55%), Gaps = 7/244 (2%)

Query: 22  KVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEKVEKVAAHWREQGADVVAIKADVSR 81
           KV L+TG + GIG +    +A + A++V+SDI  E   +V     + G+  + + ADVS+
Sbjct: 5   KVALVTGGSSGIGRSAALLYAREGAKVVVSDIHEESGMQVVREIEQLGSQAIFVAADVSK 64

Query: 82  QQDLHAMARLAIELHGRIDVLVNCAGVNVFRDPL-QMTEEDWHRCFAIDLDGAWYGCKAV 140
             D   M + A+E  GR+DV  N AG+    + +  M+ E W +  +I+L+  +Y     
Sbjct: 65  PADCERMVQQAVEKFGRLDVAFNNAGIGGESNTIGDMSIEGWDKVISINLNSVFYCMHFQ 124

Query: 141 LPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGIRVNAIAP 200
           + QM++QG G+I+N +S            Y  AKHG++GLT+  G+EYA KGIR+NAI P
Sbjct: 125 IRQMLQQGGGAIVNNSSILGQVGFANSAAYVAAKHGVVGLTKNGGLEYASKGIRINAIGP 184

Query: 201 GYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEAPFINASCI 260
            +I+T L     +G  +     Q     HP  R+G P E+A   ++L+S++A F++ +  
Sbjct: 185 AFIKTPL----LSGMGE--ETLQFLTSKHPIGRLGAPEEIAELVIWLSSNKASFVSGAYY 238

Query: 261 TIDG 264
             DG
Sbjct: 239 AADG 242


Lambda     K      H
   0.321    0.138    0.424 

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: 148
Number of extensions: 7
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: 272
Length of database: 247
Length adjustment: 24
Effective length of query: 248
Effective length of database: 223
Effective search space:    55304
Effective search space used:    55304
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 (21.9 bits)
S2: 47 (22.7 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