GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Desulfovibrio vulgaris Hildenborough

Align ABC transporter for L-Lysine, ATPase component (characterized)
to candidate 206400 DVU0968 amino acid ABC transporter, ATP-binding protein

Query= reanno::pseudo5_N2C3_1:AO356_09895
         (257 letters)



>MicrobesOnline__882:206400
          Length = 246

 Score =  232 bits (591), Expect = 6e-66
 Identities = 128/252 (50%), Positives = 172/252 (68%), Gaps = 17/252 (6%)

Query: 8   LEIRNLHKRY---GQLEVLKGVSLTARDGDVISILGSSGSGKSTFLRCINLLENPNQGQI 64
           +  RN++K +    +L  L+ VSL    G+V+ I+G SGSGKSTFLRC+N LE  + G+I
Sbjct: 4   ISARNVNKYFYVPEELHALRDVSLDVAPGEVVVIIGPSGSGKSTFLRCLNRLEYADSGEI 63

Query: 65  LVAGEELKLKAAKNGELVAADGK-QINRLRSEIGFVFQNFNLWPHMSVLDNIIEAPRRVL 123
           L+ G ++             D K +IN +R+E+G VFQ+FNL+PH+SVL+N+  A   V 
Sbjct: 64  LIEGRDI------------LDPKCEINEVRAEVGMVFQSFNLFPHLSVLENVALAQMTVR 111

Query: 124 GQSKAEAVEVAEALLAKVGIADKRHAYPAELSGGQQQRAAIARTLAMQPKVILFDEPTSA 183
            +S+AE+ +    LL KVGIADK   YP +LSGGQQQR AIAR+LAM PK++LFDEPTSA
Sbjct: 112 KRSRAESEKKGMELLTKVGIADKHAVYPDQLSGGQQQRVAIARSLAMDPKIMLFDEPTSA 171

Query: 184 LDPEMVQEVLSVIRALAEEGRTMLLVTHEMGFARQVSSEVVFLHQGLVEEQGSPQQVFEN 243
           LDPEMV EVL V+R LA EG TM++VTHEMGFAR+V+  VVF+  G + E  +P+ +F  
Sbjct: 172 LDPEMVGEVLDVMRNLAREGMTMVVVTHEMGFAREVADRVVFMDHGAILEIATPKDLFTT 231

Query: 244 PLS-ARCKQFMS 254
             +  R K F+S
Sbjct: 232 GATHDRTKLFLS 243


Lambda     K      H
   0.317    0.132    0.363 

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: 179
Number of extensions: 7
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: 257
Length of database: 246
Length adjustment: 24
Effective length of query: 233
Effective length of database: 222
Effective search space:    51726
Effective search space used:    51726
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