GapMind for catabolism of small carbon sources

 

Alignments for a candidate for alr in Azospirillum brasilense Sp245

Align Broad specificity amino-acid racemase; Broad spectrum racemase; EC 5.1.1.10 (characterized)
to candidate AZOBR_RS08350 AZOBR_RS08350 alanine racemase

Query= SwissProt::Q88GJ9
         (409 letters)



>FitnessBrowser__azobra:AZOBR_RS08350
          Length = 378

 Score =  116 bits (291), Expect = 1e-30
 Identities = 111/369 (30%), Positives = 163/369 (44%), Gaps = 35/369 (9%)

Query: 42  SNAWVEVSASALQHNIRTLQAELAGKSKLCAVLKADAYGHGIGLVMPSIIAQGVPCVAVA 101
           + A + +   A+  N   L+  +A  ++  AV+KA+AYG G+G V+P++ A G     VA
Sbjct: 13  AGAVLTIDLGAVVANWTQLRDRVA-PAECAAVVKANAYGLGVGRVVPALAAAGCRTFVVA 71

Query: 102 SNEEARVVRASGFTGQLVRVRLASLSELEDGLQYD---------MEELVGSAEFARQADA 152
             EEA  VRA   T      R+ SL  L  G   D         +  L   A +   A A
Sbjct: 72  QFEEALAVRAVAPTN----ARVLSLGGLPAGTAPDFTAQRILPVLNHLGDIAAWQAHARA 127

Query: 153 IAARHGKTLRIHMALNSSGMSRNGVEMATWSGRGEALQITDQKHLKLVALMTHFAVEDKD 212
                   + I   +N  G+  +  E+ T  G    L+  D +       MTH A  D+D
Sbjct: 128 QGTALPAVVHIDTGMNRLGLGPD--ELDTLVGDLSRLEGVDVR-----VWMTHLACADED 180

Query: 213 DVRKGLAAFNEQTDWLIKHA--RLDRSKLTLHAANSFATLEVPEARLDMVRTGGALFG-- 268
            V       N Q     + A  RL  ++ +   ANS           D+VR G AL+G  
Sbjct: 181 SV------MNSQQLGRFRSAIGRLPAAEASF--ANSSGIFHGTAFHFDLVRPGCALYGVN 232

Query: 269 DTVPARTEYKRAMQFKSHVAAVHSYPAGNTVGYDRTFTLARDSRLANITVGYSDGYRRVF 328
            T  A    +  ++  + +  V +  +  TVGY  T  +A   ++A I VGY+DGY R  
Sbjct: 233 PTPAAENPMRGTIRLDARLLQVRNVDSPMTVGYGATHRVAARGKIATIAVGYADGYLRSL 292

Query: 329 TNKGHVLINGHRVPVVGKVSMNTLMVDVTDFPD--VKGGNEVVLFGKQAGGEITQAEMEE 386
           + +GHV +NG   PVVG+VSM+ + VDV+  PD  V  G  V L G     +   +E   
Sbjct: 293 SGRGHVFVNGVAAPVVGRVSMDLVTVDVSHLPDAAVTPGGLVELIGPNRPVDTVASEGGT 352

Query: 387 INGALLADL 395
           I   +L  L
Sbjct: 353 IGYEILTSL 361


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: 354
Number of extensions: 21
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: 378
Length adjustment: 31
Effective length of query: 378
Effective length of database: 347
Effective search space:   131166
Effective search space used:   131166
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