GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Algiphilus aromaticivorans DG1253

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_043769244.1 U743_RS14650 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>NCBI__GCF_000733765.1:WP_043769244.1
          Length = 392

 Score =  330 bits (846), Expect = 7e-95
 Identities = 184/399 (46%), Positives = 262/399 (65%), Gaps = 12/399 (3%)

Query: 1   MEKMTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHL 60
           M  + + D+DL GKR+++R D NVP+  G +  D R+RAALPT+K ALE GA V++LSHL
Sbjct: 1   MAILRMSDLDLAGKRLLIRQDLNVPISGGYITSDARLRAALPTLKQALEAGASVLVLSHL 60

Query: 61  GRPK-GEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRF 119
           GRPK G   P+ SL  VA  LSE L + V     +V D ++    EL  G++ L ENTRF
Sbjct: 61  GRPKPGHLDPDNSLTLVAAWLSEQLDRVVP----LVSDWIEGV--ELAPGQIALGENTRF 114

Query: 120 HPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFL 178
             GE +ND  L++  A L DI+VNDAFGTAHRA AS  G+A+F   + AG L+  E++ L
Sbjct: 115 AAGEKENDETLSRKMAELCDIYVNDAFGTAHRAEASTHGVARFAKVACAGPLLSAELEAL 174

Query: 179 SKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRV 238
            K   NP++P VV++GGAKVS K+ ++TNL +KAD++++GG +  TFL A G +VG S  
Sbjct: 175 GKAVANPKRPQVVIVGGAKVSTKLDLLTNLADKADQLIVGGGIANTFLAAAGFKVGKSLH 234

Query: 239 EEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGP 298
           E D +D A+ + E+ +  G +I LP D V+A +I      +V ++ D + +  M LDIGP
Sbjct: 235 EPDMLDTARAIHERIRANGGDIPLPEDVVVATEISSEARAEVRQVGD-VLDDEMILDIGP 293

Query: 299 ETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAA 358
           ++       L +A ++VWNGP+GVFE D FA GT+ +A AIA   +  A ++ GGGD+ A
Sbjct: 294 KSARALGASLRNAGSIVWNGPVGVFEYDAFAAGTRILAHAIA---DSDAFSLAGGGDTLA 350

Query: 359 AVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASIADK 397
           A++ FG+ D+ S++STGGGA LEFLEGK LP +  + ++
Sbjct: 351 AIDTFGVADRISYISTGGGAFLEFLEGKTLPAVGILEER 389


Lambda     K      H
   0.317    0.137    0.386 

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: 590
Number of extensions: 37
Number of successful extensions: 5
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: 654
Length of database: 392
Length adjustment: 34
Effective length of query: 620
Effective length of database: 358
Effective search space:   221960
Effective search space used:   221960
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 (21.6 bits)
S2: 52 (24.6 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