GapMind for catabolism of small carbon sources

 

Alignments for a candidate for alr in Halioglobus japonicus S1-36

Align Broad specificity amino-acid racemase; Broad spectrum racemase; EC 5.1.1.10 (characterized)
to candidate WP_084200507.1 C0029_RS02215 alanine racemase

Query= SwissProt::Q88GJ9
         (409 letters)



>NCBI__GCF_002869505.1:WP_084200507.1
          Length = 360

 Score =  128 bits (321), Expect = 3e-34
 Identities = 111/341 (32%), Positives = 170/341 (49%), Gaps = 31/341 (9%)

Query: 52  ALQHNIRTLQAELAGKSKLCAVLKADAYGHGIGLVMPSIIAQGVPCVAVASNEEARVVRA 111
           AL+HN+   ++   G   +C V+KA+ YGHG GL +   +      +AVA  EEA  +R 
Sbjct: 12  ALRHNLAHARSLAPGARTMC-VVKANGYGHG-GLAIAQALEAHTDALAVACIEEALELRE 69

Query: 112 SGFTGQLVRVR-LASLSELEDGLQYDMEELVGS---AEFARQADAIAARHGKTLRIHMAL 167
            G    ++ +  + +  EL    ++++  ++ +    ++  QA  +AA     L++    
Sbjct: 70  GGVRCPILLLEGVFAADELPLAAEHNLWVMIDNHKQLQWLEQAQ-LAAPITCWLKV---- 124

Query: 168 NSSGMSRNGVEMATWSGRGEALQITDQKHLKLVALMTHFAVED---KDDVRKGLAAFNEQ 224
             +GM R GV+          L     +  +LV   THFA  D    D   + +  FN  
Sbjct: 125 -DTGMHRLGVQPEEAEAFHSRLMACANRTGELVTC-THFASADDLSSDQTARQIELFNAI 182

Query: 225 TDWLIKHARLDRSKLTLHAANSFATLEVPEARLDMVRTGGALFGDT----VPARTEYKR- 279
           T      A L   +    AANS   L  P++  D +R G  L+G++      A TE  R 
Sbjct: 183 T------ASLPGPR---SAANSPGLLGWPDSHFDWIRPGYMLYGNSPFAQAHANTEALRP 233

Query: 280 AMQFKSHVAAVHSYPAGNTVGYDRTFTLARDSRLANITVGYSDGYRRVFTNKGHVLINGH 339
            M   S V ++     G++VGY  T+T  R SR+A I++GY DGY R+  N   VLING 
Sbjct: 234 VMTLTSAVISLRDLAPGDSVGYAATWTAERPSRIATISIGYGDGYPRLANNGTPVLINGQ 293

Query: 340 RVPVVGKVSMNTLMVDVTDFPDVKGGNEVVLFGKQ-AGGEI 379
           RVP+VG+VSM+ + VDVTD  +V  G+E +L+G Q   GE+
Sbjct: 294 RVPLVGRVSMDMITVDVTDLSEVAIGDEAILWGPQLTAGEV 334


Lambda     K      H
   0.318    0.132    0.377 

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: 344
Number of extensions: 11
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: 409
Length of database: 360
Length adjustment: 30
Effective length of query: 379
Effective length of database: 330
Effective search space:   125070
Effective search space used:   125070
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: 50 (23.9 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