GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Brucella inopinata BO1

Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_008507916.1 BIBO1_RS13055 aspartate aminotransferase family protein

Query= SwissProt::P38021
         (401 letters)



>NCBI__GCF_000182725.1:WP_008507916.1
          Length = 403

 Score =  243 bits (620), Expect = 7e-69
 Identities = 141/387 (36%), Positives = 205/387 (52%), Gaps = 9/387 (2%)

Query: 14  TSHYGANNYHPLPIVISEALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPKIIQALKDQAD 73
           T H   + Y+   +      G W+   +G  Y+D  +  +  + GH HP +++ LK QA+
Sbjct: 6   TVHPLYDTYNRAALRFERGEGIWLITEDGERYIDFAAGIAVNSLGHSHPHLVETLKTQAE 65

Query: 74  KITLTSRAFHNDQLGPFYEKTAKLTGKEMILPMNTGAEAVESAVKAARRWAYEVKGVADN 133
           K+   S  +          +  + T  + +   N+GAEA+E A+K ARR+ Y V G  + 
Sbjct: 66  KLWHLSNIYEIPAQEKLGRRLVENTFADKVFFTNSGAEALECAIKTARRYQY-VSGHPE- 123

Query: 134 QAEIIACVGNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIPYGDVEALRQAITPNTAAF 193
           +  II   G FHGRT+  ++   + +Y  GFGP + G   +P+GD  ALR AITP TA  
Sbjct: 124 RFRIITFEGAFHGRTLATIAAGGQAKYLEGFGPKVEGFDQVPFGDEAALRAAITPETAGI 183

Query: 194 LFEPIQGEAGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRTGKTFACDWDGIVPDM 253
           L EPIQGE G+   PE FL+    IC E  +L + DE+QTG+GRTGK FA +W GI PD+
Sbjct: 184 LLEPIQGEGGLRAFPEEFLRLVRQICDENGLLLLLDEVQTGVGRTGKFFAHEWAGIRPDI 243

Query: 254 YILGKALGGGVFPISCIAADREILGVFNPGSHGSTFGGNPLACAVSIASLEVLEDEKLAD 313
             + K +GGG FPI    A  E       G HG+T+GGNPL  AV  A L+V+  +   +
Sbjct: 244 MAIAKGIGGG-FPIGACLATAEAAKGMTAGMHGTTYGGNPLGMAVGNAVLDVVLADGFME 302

Query: 314 RSLELGEYFKSELESIDS---PVIKEVRGRGLFIGVELTEAARPYCERLKEEGLLCKETH 370
                    K  L S+      V+ E+RGRGL +G++         + L++E +L     
Sbjct: 303 NVQATALVMKQGLASLVDRYPNVVSEIRGRGLLMGLKCVVPNTSLIQALRDEHVLSVGAG 362

Query: 371 DTVIRFAPPLIISKEDLDWAIEKIKHV 397
           D V+R  PPLI + E+   A E +KH+
Sbjct: 363 DNVVRLLPPLITTPEE---AREALKHI 386


Lambda     K      H
   0.318    0.136    0.401 

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: 413
Number of extensions: 20
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 401
Length of database: 403
Length adjustment: 31
Effective length of query: 370
Effective length of database: 372
Effective search space:   137640
Effective search space used:   137640
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 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