GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2555 in Marinobacter adhaerens HP15

Align ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized)
to candidate GFF2974 HP15_2918 glutamine ABC transporter, periplasmic glutamine-binding protein

Query= reanno::acidovorax_3H11:Ac3H11_2555
         (249 letters)



>FitnessBrowser__Marino:GFF2974
          Length = 252

 Score =  130 bits (326), Expect = 3e-35
 Identities = 77/236 (32%), Positives = 123/236 (52%), Gaps = 6/236 (2%)

Query: 13  AAAAFCTTGAQAQDNVLRVGTDATFPPMEFV--ENGKRTGFDIELVEAIAKTMGKQVEWV 70
           A+ A            LRV TD +F P E +  E G+  GFD+E++  +A   G +++  
Sbjct: 11  ASLALTVAAGTVSAETLRVVTDPSFVPFEMMDQETGEMIGFDMEIIREVADRAGFEIDLN 70

Query: 71  DIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYAGGLVVMVKADNKAINKLAD 130
            +DF G+IP L +   D+A++ I IT+ER+++VDF+D YY  GL ++V+  N  +++  D
Sbjct: 71  TMDFNGIIPALQTGNVDIAIAGITITEEREEIVDFSDPYYDSGLRILVREGNDDVSEFDD 130

Query: 131 LDGKKVSVQVGTKSVSYLTEKFPKVQRVEVEKNQEMFNLVDIGRA-DAAVTGKPAAFQYV 189
           L+GKK+  ++G+ S  YL +       V          +  + RA DA     P    + 
Sbjct: 131 LEGKKIGTKIGSTSYDYLVKNLDADDGVTPYPGSSDMYMALMSRAIDAVFYDAPNVGYFA 190

Query: 190 RTRPGLRV--LDEQLTTEEYGMALRKDTPELTKAVNGAITKLKADGTYAAIVKKWF 243
           RT+   +V  +      ++YG+AL K   E    VN A+  +K DGTY  I +KWF
Sbjct: 191 RTKGEGKVTTVGPLYEGQQYGIAL-KSGSEWVDDVNEALAAMKEDGTYKTIYEKWF 245


Lambda     K      H
   0.317    0.133    0.369 

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: 162
Number of extensions: 12
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: 249
Length of database: 252
Length adjustment: 24
Effective length of query: 225
Effective length of database: 228
Effective search space:    51300
Effective search space used:    51300
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: 46 (22.3 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