GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03040 in Lactobacillus shenzhenensis LY-73

Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_022529299.1 L248_RS06280 amino acid ABC transporter ATP-binding protein

Query= reanno::pseudo1_N1B4:Pf1N1B4_3435
         (254 letters)



>NCBI__GCF_000469325.1:WP_022529299.1
          Length = 248

 Score =  229 bits (585), Expect = 3e-65
 Identities = 119/246 (48%), Positives = 167/246 (67%), Gaps = 11/246 (4%)

Query: 4   LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLN 63
           L+VQ+LHK +G HEVLK ++L    G+V+SIIG+SGSGKST LR INLLEQP  G IL +
Sbjct: 7   LQVQNLHKSFGDHEVLKDINLDVHKGEVMSIIGASGSGKSTLLRNINLLEQPTGGDILFH 66

Query: 64  NEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSK 123
            + +            +D   +   R+++ MVFQ FNL++++  ++N+M     VL    
Sbjct: 67  EKSI-----------LSDDFDVTLYRAKVGMVFQSFNLFNNLNVLQNVMVGQTTVLKRDA 115

Query: 124 TEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPE 183
             A+  A   L +VG+A   +A P  +SGG+QQRVAIARA AM+PEV+LFDEPTSALDPE
Sbjct: 116 AAAKTHAMELLERVGMAPYVNAKPDQLSGGQQQRVAIARAEAMDPEVLLFDEPTSALDPE 175

Query: 184 LVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSE 243
           +V +VL  M +LA  G TM++VTHEM FAR+VS+ + F++ GV+ E+G P ++  +PQ +
Sbjct: 176 MVDEVLNTMSSLAHTGLTMIIVTHEMQFARDVSDVVCFMNDGVLAETGTPEQIFEHPQEQ 235

Query: 244 RLQQFL 249
           R Q+FL
Sbjct: 236 RTQEFL 241


Lambda     K      H
   0.317    0.131    0.366 

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: 214
Number of extensions: 8
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: 254
Length of database: 248
Length adjustment: 24
Effective length of query: 230
Effective length of database: 224
Effective search space:    51520
Effective search space used:    51520
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 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