GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruH in Caldicellulosiruptor hydrothermalis 108

Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate WP_013403486.1 CALHY_RS08135 pyridoxal phosphate-dependent aminotransferase

Query= BRENDA::Q9HUI9
         (393 letters)



>NCBI__GCF_000166355.1:WP_013403486.1
          Length = 397

 Score =  204 bits (519), Expect = 4e-57
 Identities = 128/393 (32%), Positives = 199/393 (50%), Gaps = 15/393 (3%)

Query: 1   MRYSDFTQRIAGDGAAAWDIHYRALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLA 60
           M+YS     I+     A D   + L   E GE ++    G+PDFDTP  I  AAI +++ 
Sbjct: 1   MKYSQRALNISASPTLAIDSLAKKLK--EAGENVIGFGAGEPDFDTPDNIKYAAISAIVK 58

Query: 61  GNTHYADVRGKRALRQRIAERHRRRSGQAVDAEQVVVLAGAQCALYAVVQCLLNPGDEVI 120
           G T Y  V G   L++ IA+ ++         ++VVV  GA+ +L  V   LLN GDEV+
Sbjct: 59  GYTKYTPVAGISCLKEAIAKYYKENYEVDYSPDEVVVSNGAKHSLMNVFFALLNDGDEVL 118

Query: 121 VAEPMYVTYEAVFGACGARVVPVPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGA 180
           +  P +VTY  +    G +VV VP   E  +++   ++    T +T+A+ LNSP NP+G 
Sbjct: 119 LPSPYWVTYPELIKLAGGKVVVVPTTKEKNYKITLSDLEKYTTSKTKAIVLNSPSNPTGM 178

Query: 181 SLPRATWEALAELCMAHDLWMISDEVYSELLFDG-EHVSPASLPGMA-DRTATLNSLSKS 238
                  + + E C+  +++++SDE+Y +L++DG +H+S AS+   A +    +N +SKS
Sbjct: 179 VYTYEELKQIVEFCIEREIFIVSDEIYDKLIYDGKKHISAASINEKAKEFVIVVNGVSKS 238

Query: 239 HAMTGWRVGWVVGPAALCAHLENLALCMLYGSPEFIQDAACTALEAPLPELEAMREAYRR 298
           +AMTGWR+G+ +        + NL            Q AA  AL  P   ++ M   + +
Sbjct: 239 YAMTGWRIGYTLSNKEFTKIMSNLQSHTTSNPNSIAQYAAYEALVGPQDSVKKMICEFEK 298

Query: 299 RRDLVIECLADSPGLRPLRPDGGMFVMVDIRPTG---------LSAQAFADRLLDRHGVS 349
           RRDL+   + D+  L  L+P+G  ++ VDI              SA  FA  LL+   V+
Sbjct: 299 RRDLIYSLVNDTKFLSALKPEGAFYIWVDISAAVGKSFEGKLIDSANTFAKLLLEVEKVA 358

Query: 350 VLAGEAFGPSAAGHIRLGLVLGAEPLREACRRI 382
           V+  E FG     HIRL      + +RE   RI
Sbjct: 359 VVPSEGFG--MENHIRLSYATSEKNIREGLERI 389


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: 339
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: 393
Length of database: 397
Length adjustment: 31
Effective length of query: 362
Effective length of database: 366
Effective search space:   132492
Effective search space used:   132492
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