GapMind for catabolism of small carbon sources

 

Alignments for a candidate for alr in Klebsiella michiganensis M5al

Align Broad specificity amino-acid racemase; Broad spectrum racemase; EC 5.1.1.10 (characterized)
to candidate BWI76_RS01920 BWI76_RS01920 alanine racemase

Query= SwissProt::Q88GJ9
         (409 letters)



>FitnessBrowser__Koxy:BWI76_RS01920
          Length = 359

 Score =  106 bits (264), Expect = 1e-27
 Identities = 105/343 (30%), Positives = 163/343 (47%), Gaps = 32/343 (9%)

Query: 44  AWVEVSASALQHNIRTLQAELAGKSKLCAVLKADAYGHGI---GLVMPSIIAQGVPCVAV 100
           A V ++  AL+HN++ L+ ELA  SKL AV+KA+AYGHG+      +P   A GV     
Sbjct: 4   ATVVINRRALRHNLQRLR-ELAPASKLVAVVKANAYGHGLLETARTLPDADAFGV----- 57

Query: 101 ASNEEARVVRASGFTGQLVRVRLASLSELEDGLQYDMEELVGSAEFARQADAIA-ARHGK 159
           A  EEA  +RA G    ++   L    E  D      + L  +     Q  A+  A   +
Sbjct: 58  ARLEEALRLRAGGIAQPILL--LEGFFEAADLPVISTQRLHTAVHSPEQLAALEEADLPE 115

Query: 160 TLRIHMALNSSGMSRNGVEMATWSGRGEAL--QITDQKHLKL-VALMTHFAVEDKDDVRK 216
            + + M L++ GM R GV       + EA   +++  K+++  V +++HFA  D+ +   
Sbjct: 116 PVTVWMKLDT-GMHRLGV----LPEQAEAFYQRLSQCKNVRQPVNVVSHFARADEPEC-- 168

Query: 217 GLAAFNEQTDWLIKHARLDRSKLTLHAANSFATLEVPEARLDMVRTGGALFG------DT 270
              A   Q D             ++ A+     L  P++  D  R G  L+G       +
Sbjct: 169 --GATERQLDIFTTFTEGKPGLRSIAASGGI--LLWPQSHFDWARPGIILYGVSPLDGGS 224

Query: 271 VPARTEYKRAMQFKSHVAAVHSYPAGNTVGYDRTFTLARDSRLANITVGYSDGYRRVFTN 330
             A    +  M   S + AV  + AG  VGY  T+   RD+RL  + +GY DGY R   +
Sbjct: 225 TGADFGCQPVMSLTSSLIAVREHKAGEPVGYGGTWISERDTRLGVVAMGYGDGYPRAAPS 284

Query: 331 KGHVLINGHRVPVVGKVSMNTLMVDVTDFPDVKGGNEVVLFGK 373
              VL+NG  VP+VG+V+M+ + VD+      K G+ VVL+G+
Sbjct: 285 GTPVLVNGREVPIVGRVAMDMICVDLGPEAQDKSGDPVVLWGE 327


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: 322
Number of extensions: 13
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: 359
Length adjustment: 30
Effective length of query: 379
Effective length of database: 329
Effective search space:   124691
Effective search space used:   124691
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 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