GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Halioglobus japonicus S1-36

Align succinylornithine transaminase; EC 2.6.1.81 (characterized)
to candidate WP_084199387.1 C0029_RS09770 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= CharProtDB::CH_002469
         (406 letters)



>NCBI__GCF_002869505.1:WP_084199387.1
          Length = 467

 Score =  186 bits (472), Expect = 1e-51
 Identities = 135/409 (33%), Positives = 195/409 (47%), Gaps = 36/409 (8%)

Query: 20  PAPFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYT 79
           PA FI  R EG  +WD  G +YIDF  G A N LG+ HPE+ EA++E   ++        
Sbjct: 42  PAQFIVGRAEGDYVWDLDGNQYIDFQNGWATNPLGNCHPEILEAVHEAQRQYGFQWEHPL 101

Query: 80  NEPVLRLAKKLIDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNAFH 139
             P+      ++ +    R  F  SG EA E+A+ LA      RY      IV+F + FH
Sbjct: 102 RIPLAERLASIMPSGSLPRFSFEVSGTEAAESAIHLALCHTQRRY------IVSFTSCFH 155

Query: 140 GRTLFT--VSA--GGQPAYSQDFA------------PLPADIRHAAYNDIN--------S 175
           G  L T  VSA       Y + +A             +PA +  A Y +          +
Sbjct: 156 GEGLGTKMVSAYNSDNNLYMEGWAGGVLKAPFPYSEEIPAGMDQAQYTEYCLWYIETHLT 215

Query: 176 ASALIDDSTCAVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGEL 235
              +  ++  A++VEP   EGG    S AF+QGLR +C++ + LLI DEV TG+GRTG +
Sbjct: 216 EYVVPAENIAAILVEPGLAEGGNWIPSKAFMQGLRRICDKFDWLLIADEVLTGLGRTGTM 275

Query: 236 YAYMHYGVTPDLLTTAKALGGGF-PVGALLATEECARVMTVGTHGTTYGGNPLASAVAGK 294
           +A  H+ V PD+L   K L GG  P   + A +E        T G+T+ G P   A A K
Sbjct: 276 WAVEHFDVVPDILVAGKNLSGGIEPCAGVAARDEILGDNPRATAGSTFAGTPGGCAAALK 335

Query: 295 VLELINTPEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNA-----DYAG 349
            LE+     +L   +      ++R++    RY + S+VRGLGLL+G    A     +   
Sbjct: 336 TLEIYERDAVLTHTQHLAGVAMQRMSDWESRYEIVSQVRGLGLLLGVSFRAGREDIEDFH 395

Query: 350 QAKQISQEAAKAGVMVLIAGGNVVRFAPALNVSEEEVTTGLDRFAAACE 398
            A+ +  E  K G+  +      VR  PALN++E+ +  GL R   A E
Sbjct: 396 IARSVRDEMLKRGLWAICDNEPQVRMYPALNMAEDVLLEGLSRMEEAIE 444


Lambda     K      H
   0.319    0.136    0.407 

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: 468
Number of extensions: 22
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: 406
Length of database: 467
Length adjustment: 32
Effective length of query: 374
Effective length of database: 435
Effective search space:   162690
Effective search space used:   162690
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 (21.8 bits)
S2: 51 (24.3 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