GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Jannaschia aquimarina GSW-M26

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate WP_043919874.1 jaqu_RS15290 ABC transporter ATP-binding protein

Query= TCDB::P73721
         (252 letters)



>NCBI__GCF_000877395.1:WP_043919874.1
          Length = 376

 Score =  152 bits (383), Expect = 1e-41
 Identities = 89/246 (36%), Positives = 137/246 (55%), Gaps = 13/246 (5%)

Query: 7   PLISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLE 66
           PLIS   + K +G    +  +T +I+P++  +++GPSGCGK+T +R L   E +SGGR+ 
Sbjct: 17  PLISCQDVTKRYGEFTAIERLTLDIFPREFFALLGPSGCGKTTLMRMLGGFEDVSGGRIT 76

Query: 67  VAGVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAK-- 124
           + G D++G   +++        V M+FQ + LFPHLTV  NL      + R  MA+ +  
Sbjct: 77  IDGQDMAGIPPNKR-------AVNMMFQSYALFPHLTVWDNLAFG---LKRSDMAKDQIG 126

Query: 125 DRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGE 184
           DR    L  V L   A   P QLSGGQKQRVA+AR L   P++LL DEP  ALD +L  +
Sbjct: 127 DRVEAMLKLVQLQKFAKRKPHQLSGGQKQRVALARALAKGPKLLLLDEPLGALDKKLRQQ 186

Query: 185 VLNVMKQLAEE-GMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLR 243
               +  + E+ G T  +VTH+ + A  V++R+   ++G I +   P  ++  P S  + 
Sbjct: 187 TQFELMDIQEKTGTTFVIVTHDQEEAMTVASRIAVMDEGRIVQVDTPGRIYEAPNSVYVA 246

Query: 244 AFLSRI 249
            F+  +
Sbjct: 247 DFIGDV 252


Lambda     K      H
   0.321    0.139    0.397 

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: 225
Number of extensions: 12
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: 252
Length of database: 376
Length adjustment: 27
Effective length of query: 225
Effective length of database: 349
Effective search space:    78525
Effective search space used:    78525
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: 48 (23.1 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