GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpF in Bacillus altitudinis 41KF2b

Align 2-methyl-aconitate isomerase; Cis-trans isomerase; EC 5.3.3.- (characterized)
to candidate WP_035701937.1 BA79_RS07240 3-methylitaconate isomerase

Query= SwissProt::Q937N7
         (396 letters)



>NCBI__GCF_000691145.1:WP_035701937.1
          Length = 376

 Score =  208 bits (530), Expect = 2e-58
 Identities = 139/388 (35%), Positives = 202/388 (52%), Gaps = 36/388 (9%)

Query: 8   KIPATYIRGGTSKGVFFRLQDLPETAQVPGPARDALLMRVIGSPDPYGKQIDGMGAATSS 67
           K+P T +RGGTSKGVF +  D P          +  L+ ++GSPD    Q+DG+G   S 
Sbjct: 3   KVPITIMRGGTSKGVFIQANDAPYEHD----ELEEFLLDIMGSPDRL--QVDGIGGGNSL 56

Query: 68  TSKTVILSKSTRPDHDVDYLFGQVSIDQPFVDWSGNCGNLSAAVGPFAISAGLVDASRIP 127
           TSK  I+ K+TRPD DV+Y F QVSI++ FVD+ GNCGN+S+AVGP+AI  GLV A    
Sbjct: 57  TSKVAIIDKATRPDVDVNYTFAQVSINERFVDFKGNCGNISSAVGPYAIIKGLVQAV--- 113

Query: 128 HNGVAVVRIWQANIGKTIIGHVPVTNGEVQETGDFELDGVTFPAAEVQLEFMDPAAEEEG 187
              V  VRI   N  K I+  V V NGEV+  G  E+ GV    + + L F  P   E  
Sbjct: 114 -EPVTTVRILNTNTNKIIVAEVEVENGEVKFEGQAEIPGVKGTGSPIYLSFEKP---EGA 169

Query: 188 AGGAMFPTGNVVDDLEVPAVGTLKATMINAGIPTIFVNAESIGYTGTEL----QDAINSD 243
             G  FPTGN +D ++    G +  ++++   P  FV A+ I   GTEL     D +  D
Sbjct: 170 VTGKTFPTGNKMDTIQT-KFGEIPISIVDIANPIAFVRAKDIQLKGTELPEEFTDELLDD 228

Query: 244 TRALAMFEDHPCYGALRMGLIKNVDEAAKRQH--TPKVAFVRQAGDYVASSGKKVAAADV 301
              +       C+ A +        E A  Q    PK+A + +  DYV ++G    AAD+
Sbjct: 229 LEEIRSIAAEMCHFAPK--------ELATLQSPAVPKLAIISEPADYVDTNGILRRAADM 280

Query: 302 DLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGERNAVRFGHPSGTLRVGA 361
           D++VR LSM + H A+  T +V +  +  +  TL       G+ + +R GHP+G ++   
Sbjct: 281 DIIVRMLSMQRPHQALAITGSVCVSASCFMDQTL-PAQLFEGQDDTLRIGHPAGIMQTEI 339

Query: 362 EAQQVDGEWAVKKAIMSRSARVLMEGWV 389
           +  Q        +  + R+AR +++G V
Sbjct: 340 DISQ-------NRVKVIRTAREILDGVV 360


Lambda     K      H
   0.317    0.134    0.394 

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: 338
Number of extensions: 18
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: 396
Length of database: 376
Length adjustment: 30
Effective length of query: 366
Effective length of database: 346
Effective search space:   126636
Effective search space used:   126636
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.

Links

Downloads

Related tools

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