GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ligJ in Magnetospirillum magneticum AMB-1

Align subunit of 4-oxalomesaconate hydratase (EC 4.2.1.83) (characterized)
to candidate WP_011382698.1 AMB_RS01275 amidohydrolase

Query= metacyc::MONOMER-3243
         (342 letters)



>NCBI__GCF_000009985.1:WP_011382698.1
          Length = 342

 Score =  617 bits (1591), Expect = 0.0
 Identities = 285/342 (83%), Positives = 317/342 (92%)

Query: 1   MIIDVHGHYTTAPAALGAWRDLQIAGLKDPSKTPSVADLKISDDEIRETIETNQLRLMKE 60
           MIID+HGHYTTAP AL  WR+ QIAGLKDP++ P V++LKISDDE+RE+IETNQL  MKE
Sbjct: 1   MIIDIHGHYTTAPKALEEWRNRQIAGLKDPAQAPKVSELKISDDELRESIETNQLAKMKE 60

Query: 61  RGSDLTIFSPRASFMAHHIGDFQTSSTWAAICNELCFRVSELFPDHFIPAAMLPQSPGVD 120
           RGSDLTIFSPRASFMAHHIGDFQTSSTWAAICNELC RV++LFPD+FI AAMLPQSPGVD
Sbjct: 61  RGSDLTIFSPRASFMAHHIGDFQTSSTWAAICNELCARVAKLFPDNFIGAAMLPQSPGVD 120

Query: 121 PATCIPELVKCVEQYGNVGLNLNPDPSGGHWTSPPLSDKSWYPIYEKMVEYDIPAMIHVS 180
           P TCIPE+ KCV++YG V +NLNPDPSGGHWTSPPLSD+SWYPIYE MVEY +PAM+HVS
Sbjct: 121 PKTCIPEIEKCVKEYGFVAINLNPDPSGGHWTSPPLSDRSWYPIYEAMVEYGLPAMVHVS 180

Query: 181 TSCNSCFHTTGSHYLNADTTAFMQCLTSDLFKDFPTLKFLIPHGGGAVPYHWGRFRGLAQ 240
           TSCN+CFHTTG+HYLNADTTAFMQCLTSDLFKDFP LKF+IPHGGGAVPYHWGRFRGLAQ
Sbjct: 181 TSCNACFHTTGAHYLNADTTAFMQCLTSDLFKDFPELKFIIPHGGGAVPYHWGRFRGLAQ 240

Query: 241 EMKKPLLEEHLLNNIYFDTCVYHQPGINLLTEVIPTKNILFASEMIGAVRGIDPQTGHYY 300
           E+KKPLL +HLLNNI+FDTCVYHQPGI+LLT+VIP  NILFASEMIGAVRGIDP+TGHYY
Sbjct: 241 ELKKPLLRDHLLNNIFFDTCVYHQPGIDLLTKVIPVDNILFASEMIGAVRGIDPETGHYY 300

Query: 301 DDTKRYIEATQNLTADEKHAVYEGNARRVFTRLDKALKAKGL 342
           DDTKRYIEAT NL+ +++H VYEGNARRV+ RLD ALKAKGL
Sbjct: 301 DDTKRYIEATLNLSPEDRHKVYEGNARRVYPRLDAALKAKGL 342


Lambda     K      H
   0.320    0.137    0.429 

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: 528
Number of extensions: 14
Number of successful extensions: 1
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: 342
Length of database: 342
Length adjustment: 29
Effective length of query: 313
Effective length of database: 313
Effective search space:    97969
Effective search space used:    97969
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: 49 (23.5 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