GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__azobra:AZOBR_RS24310 AZOBR_RS24310
           3-methylitaconate isomerase
          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.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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