GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Thiomicrospira cyclica ALM1

Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_013835847.1 THICY_RS06630 aspartate aminotransferase family protein

Query= curated2:Q89RB7
         (404 letters)



>NCBI__GCF_000214825.1:WP_013835847.1
          Length = 390

 Score =  256 bits (655), Expect = 6e-73
 Identities = 152/371 (40%), Positives = 208/371 (56%), Gaps = 11/371 (2%)

Query: 18  HNYEPIGVVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTS 77
           + Y  + V    GEG  ++D   N YLD +S  +  S GH HP I  A+ EQ+  L  TS
Sbjct: 6   NTYGRLPVTFHYGEGALLYDEQDNAYLDAVSGIAVCSLGHAHPAIAQALCEQSKTLIHTS 65

Query: 78  RAFHNDQLAPFYEEIAALTGSHKVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEIIV 137
             +H  +     +++ A++G  KV   NSGAEA E+AIK  RK+G+  KG+    A+IIV
Sbjct: 66  NLYHVAKQQQLGDKLVAISGMDKVFFGNSGAEANEAAIKMARKYGHS-KGI--SHAQIIV 122

Query: 138 CADNFHGRTLGIVGFSTDPETRGHFGPFAPGFRIIPFGDAAALEQAIT--PNTVAFLVEP 195
             ++FHGRTL  +  +   +    F P   GF  +PF +  A+  AI   PN VA LVEP
Sbjct: 123 MENSFHGRTLATLSATGSAKVHDGFYPLVEGFVRVPFDNVEAVANAIANNPNVVAILVEP 182

Query: 196 IQGEAGVIIPPAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADVTLLG 255
           +QGE GV +P  GY   +R LC  ++++L++DEIQ G+GRTGK  A QHEGI  DV  L 
Sbjct: 183 VQGEGGVHVPKPGYLKALRALCDEHDLLLMIDEIQAGIGRTGKWFAFQHEGILPDVLSLA 242

Query: 256 KALAGGFYPVSAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAAR 315
           KAL  G  P+ A L+  +      PG HG+TFGGNPLACA   A +  L     I+  A+
Sbjct: 243 KALGNG-VPIGASLARGKAAELFAPGNHGTTFGGNPLACAAGLAVIETLEYHNYIDLVAK 301

Query: 316 QGARLLEGLKDIRANT--VREVRGRGLMLAVELHPEAGRARRYCEALQGKGILAKDTHGH 373
           QGA LL   K   AN   V ++RG+G M+ ++L    G   +   AL  K +L   T G 
Sbjct: 302 QGAELLAAFKTALANIPGVVDIRGKGYMIGIQLDRPCGDLVKM--ALADK-LLINVTRGD 358

Query: 374 TIRIAPPLVIT 384
           T+R+ P  V+T
Sbjct: 359 TVRLLPTFVMT 369


Lambda     K      H
   0.319    0.136    0.405 

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: 407
Number of extensions: 22
Number of successful extensions: 5
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: 404
Length of database: 390
Length adjustment: 31
Effective length of query: 373
Effective length of database: 359
Effective search space:   133907
Effective search space used:   133907
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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