GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpF in Azospirillum thiophilum BV-S

Align 2-methyl-aconitate isomerase; Cis-trans isomerase; EC 5.3.3.- (characterized)
to candidate WP_045580431.1 AL072_RS10180 2-methylaconitate cis-trans isomerase PrpF

Query= SwissProt::Q937N7
         (396 letters)



>NCBI__GCF_001305595.1:WP_045580431.1
          Length = 405

 Score =  576 bits (1485), Expect = e-169
 Identities = 291/405 (71%), Positives = 323/405 (79%), Gaps = 9/405 (2%)

Query: 1   MTHVPQIKIPATYIRGGTSKGVFFRLQDLPETAQVPGPARDALLMRVIGSPDPYGKQIDG 60
           M   PQI+IPATY+RGGTSKG+FFRL DLPE  +V G ARD L +RVIGSPDPY + IDG
Sbjct: 1   MASAPQIRIPATYMRGGTSKGIFFRLDDLPERCRVAGAARDRLFLRVIGSPDPYARHIDG 60

Query: 61  MGAATSSTSKTVILSKSTRPDHDVDYLFGQVSIDQPFVDWSGNCGNLSAAVGPFAISAGL 120
           MG ATSSTSK VILSKS RP HDVDYL+GQVSID  FVDWSGNCGNLS A G FAI AGL
Sbjct: 61  MGGATSSTSKAVILSKSARPGHDVDYLYGQVSIDSAFVDWSGNCGNLSTAAGAFAIHAGL 120

Query: 121 VDASRIPHNGVAVVRIWQANIGKTIIGHVPVTNGEVQETGDFELDGVTFPAAEVQLEFMD 180
           +D +R+P NGV  VRIWQANIGKTI+ HVP T G VQETGDFELDGVTFPAAE+ LEF+D
Sbjct: 121 MDPARVPENGVCTVRIWQANIGKTIVAHVPATGGLVQETGDFELDGVTFPAAEIVLEFLD 180

Query: 181 PAAEEE-----GAGGAMFPTGNVVDDLEVP----AVGTLKATMINAGIPTIFVNAESIGY 231
           PA E +     G  G+MFPTGN++D LEVP      G LKAT+I+AGIPTIFV A  +GY
Sbjct: 181 PAEEGDSGGAGGGNGSMFPTGNLIDTLEVPDSLVPGGRLKATLIDAGIPTIFVAAADLGY 240

Query: 232 TGTELQDAINSDTRALAMFEDHPCYGALRMGLIKNVDEAAKRQHTPKVAFVRQAGDYVAS 291
            GTELQ+AIN D  ALA FE     GALRMGLIK   EAA+RQHTPK+AFV    D+V S
Sbjct: 241 RGTELQEAINGDAAALARFEALRTIGALRMGLIKEPGEAARRQHTPKIAFVAPPADHVVS 300

Query: 292 SGKKVAAADVDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGERNAVRFG 351
           SG+ V A +VDLLVRALSMGKLHHAMMGTA+VAI  AAA+PGTLVNLAAGGG R AVRFG
Sbjct: 301 SGRTVGAGEVDLLVRALSMGKLHHAMMGTASVAIAAAAAVPGTLVNLAAGGGARTAVRFG 360

Query: 352 HPSGTLRVGAEAQQVDGEWAVKKAIMSRSARVLMEGWVRVPGDAF 396
           HPSG+LRVGAEA  VDG W V KA+MSRSAR+LMEGWVRVP D+F
Sbjct: 361 HPSGSLRVGAEAVPVDGRWTVTKAVMSRSARILMEGWVRVPADSF 405


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: 568
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: 405
Length adjustment: 31
Effective length of query: 365
Effective length of database: 374
Effective search space:   136510
Effective search space used:   136510
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.

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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