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_109968747.1 DK846_RS09780 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme

Query= BRENDA::Q9HUI9
         (393 letters)



>NCBI__GCF_003173355.1:WP_109968747.1
          Length = 385

 Score =  219 bits (557), Expect = 1e-61
 Identities = 119/352 (33%), Positives = 198/352 (56%), Gaps = 2/352 (0%)

Query: 32  EEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQAVD 91
           E+++ L VG+PD+ TP  I +AAI S+  G+T Y    G   LR+ ++     R   + D
Sbjct: 28  EDVISLGVGEPDYTTPWHICEAAITSIEQGHTSYTSNTGLETLRRDLSSFLNNRYQISYD 87

Query: 92  A-EQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSENG 150
              +++V  G   AL   ++ +++PGDE +V +P+YV+Y       G + V +P   ++ 
Sbjct: 88  PLSEMIVTTGVSEALDIAIRAVIDPGDEALVVDPIYVSYGPCVTLAGGKPVLMPCLEKDH 147

Query: 151 FRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMISDEVYSEL 210
           FR+  + +   ITP+++ + LN P+NPSGA + +   + +A++ + HDL ++SDEVY+EL
Sbjct: 148 FRLTPDLLMEHITPKSKVLILNFPNNPSGAVMRKEDIKGIADVAIDHDLLILSDEVYAEL 207

Query: 211 LFDGEHVSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCMLYGS 270
            ++G+H + AS+ G+ +RT TL+  SK+ AMTGWR+G+   P  + A    +   ++  +
Sbjct: 208 TYEGKHCAVASVDGLWERTVTLSGFSKAFAMTGWRLGYFCAPKEITAAALKIHQYIMLSA 267

Query: 271 PEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFVMVDIRP 330
           P   Q  A  AL      +E M   Y  RR+L ++ L +  GL    P+G  +    ++ 
Sbjct: 268 PTMAQYGAIEALRHGQDPMEQMVREYHMRRNLFVDGL-NRIGLPCHLPEGAFYAFPSVKQ 326

Query: 331 TGLSAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVLGAEPLREACRRI 382
           TGLS Q FA+RL+   GV+V+ G  FG +  GH+R    +    L EA  R+
Sbjct: 327 TGLSDQEFAERLITEAGVAVVPGSVFGTAGEGHVRCAYAVSRNDLSEAIARM 378


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: 357
Number of extensions: 14
Number of successful extensions: 3
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: 385
Length adjustment: 30
Effective length of query: 363
Effective length of database: 355
Effective search space:   128865
Effective search space used:   128865
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