GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruH in Methanospirillum lacunae Ki8-1

Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate WP_109968729.1 DK846_RS09685 pyridoxal phosphate-dependent aminotransferase

Query= BRENDA::Q9HUI9
         (393 letters)



>NCBI__GCF_003173355.1:WP_109968729.1
          Length = 377

 Score =  212 bits (539), Expect = 2e-59
 Identities = 126/368 (34%), Positives = 197/368 (53%), Gaps = 8/368 (2%)

Query: 15  AAAWDIHYRALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRAL 74
           +A  +I  +A      G +++ LS+G+PDF TPA I  A ID+L  G THYA  +G  +L
Sbjct: 14  SATIEITDKARRLQASGVDVISLSIGEPDFPTPAHITAACIDALNRGETHYAPGKGIPSL 73

Query: 75  RQRIAERHRRRSGQAVDAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFG 134
              I+E+    +G +   +QV+V  GA+ A+Y   + +LNPGDE ++ +P +V+YE    
Sbjct: 74  LSAISEKIEAENGFSCTNDQVIVTCGAKDAIYEACEAVLNPGDEAVILDPSWVSYEPCIQ 133

Query: 135 ACGARVVPVPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELC 194
             G   V  P+  +  F+V+ + +   I  +TR + +NSP NPSG+ L R +   ++++C
Sbjct: 134 IAGGTPVHHPLHKKT-FQVE-DSLLEKINNKTRMIIVNSPSNPSGSVLNRESLRLVSDIC 191

Query: 195 MAHDLWMISDEVYSELLFDGEHVSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAA 254
             HDL  +SDE+Y +L++   H S A  PGM DRT T+N  SK++AMTGWR+G+ V P  
Sbjct: 192 QDHDLVALSDEIYEKLVYGQIHFSLAMFPGMVDRTITINGFSKAYAMTGWRLGYAVAPKE 251

Query: 255 LCAHLENLALCMLYGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLR 314
           +  ++  +    +     F    A  AL+ P   +  MR  + RRR+ V+  L D  G+ 
Sbjct: 252 ILGYMNKVQQHTISHPTTFAMFGAVAALKGPQQCISEMRNEFERRREFVLNRLMDM-GIG 310

Query: 315 PLRPDGGMFVMVDIRPTGLSAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVLGAEP 374
               +G  +  + +     S    A+R L+   V+V  G AF  +  G IRL      + 
Sbjct: 311 YAPAEGAFYAYLKVDGDDAS---IANRWLEEAHVAVTPGVAF--NTPGWIRLSYAASMDT 365

Query: 375 LREACRRI 382
           L EA  RI
Sbjct: 366 LAEAMNRI 373


Lambda     K      H
   0.322    0.136    0.411 

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: 379
Number of extensions: 18
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: 393
Length of database: 377
Length adjustment: 30
Effective length of query: 363
Effective length of database: 347
Effective search space:   125961
Effective search space used:   125961
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: 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