GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpF in Azospirillum brasilense Sp245

Align 2-methyl-aconitate isomerase; Cis-trans isomerase; EC 5.3.3.- (characterized)
to candidate AZOBR_RS24310 AZOBR_RS24310 3-methylitaconate isomerase

Query= SwissProt::Q937N7
         (396 letters)



>FitnessBrowser__azobra:AZOBR_RS24310
          Length = 401

 Score =  575 bits (1483), Expect = e-169
 Identities = 294/401 (73%), Positives = 321/401 (80%), Gaps = 5/401 (1%)

Query: 1   MTHVPQIKIPATYIRGGTSKGVFFRLQDLPETAQVPGPARDALLMRVIGSPDPYGKQIDG 60
           M   PQI+IPATY+RGGTSKGVFFRL DLPE  +VPG ARD L +RVIGSPDPY K IDG
Sbjct: 1   MAFAPQIRIPATYMRGGTSKGVFFRLDDLPERCRVPGEARDRLFLRVIGSPDPYAKHIDG 60

Query: 61  MGAATSSTSKTVILSKSTRPDHDVDYLFGQVSIDQPFVDWSGNCGNLSAAVGPFAISAGL 120
           MG A+SSTSK VILSKS RP HDVDYL+GQV+ID  FVDWSGNCGNLS A G FAI AGL
Sbjct: 61  MGGASSSTSKCVILSKSARPGHDVDYLYGQVAIDAAFVDWSGNCGNLSTAAGAFAIHAGL 120

Query: 121 VDASRIPHNGVAVVRIWQANIGKTIIGHVPVTNGEVQETGDFELDGVTFPAAEVQLEFMD 180
           VD +R+P NGV  VRIWQANIGKTII HVPVT G+VQETG F LDGVTFPAAE+ LEF+D
Sbjct: 121 VDPARVPENGVCTVRIWQANIGKTIIAHVPVTAGQVQETGSFALDGVTFPAAEIVLEFID 180

Query: 181 PAAE-EEGAGGAMFPTGNVVDDLEVP----AVGTLKATMINAGIPTIFVNAESIGYTGTE 235
           PA E E   GG+M PTGN +DDL+VP      G LKAT+INAGIPTIF++A  +GY GTE
Sbjct: 181 PADEGESEGGGSMLPTGNPIDDLDVPDSLVPGGRLKATLINAGIPTIFIDAADLGYRGTE 240

Query: 236 LQDAINSDTRALAMFEDHPCYGALRMGLIKNVDEAAKRQHTPKVAFVRQAGDYVASSGKK 295
            Q AIN D  ALA FE     GALRMGLI+   EAA+RQHTPK+AFV     Y ASSGK+
Sbjct: 241 SQAAINGDATALARFEALRTIGALRMGLIREPGEAARRQHTPKIAFVAPPDAYTASSGKR 300

Query: 296 VAAADVDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGERNAVRFGHPSG 355
           V A D+DLLVRALSMGKLHHAMMGTA+VAI  AAA+PGTLVN AAGGG RNAVRFGHPSG
Sbjct: 301 VEAGDIDLLVRALSMGKLHHAMMGTASVAIAAAAAVPGTLVNRAAGGGTRNAVRFGHPSG 360

Query: 356 TLRVGAEAQQVDGEWAVKKAIMSRSARVLMEGWVRVPGDAF 396
           TLRVGAEA  VDG W V KAIMSRSARVLMEGWV VP D+F
Sbjct: 361 TLRVGAEAALVDGRWTVTKAIMSRSARVLMEGWVCVPADSF 401


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: 548
Number of extensions: 17
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: 396
Length of database: 401
Length adjustment: 31
Effective length of query: 365
Effective length of database: 370
Effective search space:   135050
Effective search space used:   135050
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 17 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