GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Pseudomonas fluorescens GW456-L13

Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate PfGW456L13_4910 Acetylornithine aminotransferase (EC 2.6.1.11)

Query= curated2:Q89RB7
         (404 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4910
          Length = 413

 Score =  273 bits (697), Expect = 9e-78
 Identities = 158/375 (42%), Positives = 216/375 (57%), Gaps = 11/375 (2%)

Query: 20  YEPIGVVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTSRA 79
           Y+P+ +  ++G G  +WD  G  YLD ++  +  + GH HPKI+AA+ EQA  L  TS  
Sbjct: 32  YQPLALSFNKGLGTRLWDQAGREYLDAVAGVAVTNVGHSHPKIVAAITEQAGLLLHTSNL 91

Query: 80  FHNDQLAPFYEEIAALTGSHKVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEIIVCA 139
           +  D      +++  L G  +    NSGAEA E+A+K  R  G+  KG+  +Q  ++V  
Sbjct: 92  YSIDWQQRLAQKLTQLAGMDRAFFNNSGAEANETALKIARLHGWH-KGI--EQPLVVVME 148

Query: 140 DNFHGRTLGIVGFSTDPETRGHFGPFAPGFRIIPFGDAAALE---QAITPNTVAFLVEPI 196
           + FHGRTLG +  S  P  R  F      F  +PFGD  AL+   QA     VA L+EPI
Sbjct: 149 NAFHGRTLGTLSASDGPAVRLGFNKLPGDFVKVPFGDLGALDKVQQAFGSRIVAVLMEPI 208

Query: 197 QGEAGVIIPPAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADVTLLGK 256
           QGE+GV + P GY + VRELC   + +L+LDEIQTG+GRTG+  A QHEGI  DV  L K
Sbjct: 209 QGESGVQLAPPGYLSAVRELCNRRSWLLMLDEIQTGIGRTGQWFAFQHEGIVPDVMTLAK 268

Query: 257 ALAGGFYPVSAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAARQ 316
            L  G  P+ A L+  +      PG HGSTFGGNPLAC V    + ++ E+G++ENA  Q
Sbjct: 269 GLGNG-VPIGACLARGKAAELFTPGSHGSTFGGNPLACRVGCTVLDIVEEQGLLENARLQ 327

Query: 317 GARLLEGLKDIRAN--TVREVRGRGLMLAVELHPEAGRARRYCEALQGKGILAKDTHGHT 374
           GARLLE L+   A    V ++RG+GLM+ +EL            A +  G+L   T G+T
Sbjct: 328 GARLLERLRTELAGNPNVSQIRGQGLMIGIELKQPIRDLSLI--AARDHGLLINVTRGNT 385

Query: 375 IRIAPPLVITSDEVD 389
           IR+ PPL +   EV+
Sbjct: 386 IRLLPPLTLDEREVE 400


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: 481
Number of extensions: 22
Number of successful extensions: 6
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: 413
Length adjustment: 31
Effective length of query: 373
Effective length of database: 382
Effective search space:   142486
Effective search space used:   142486
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 Sep 17 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