GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Alkalitalea saponilacus SC/BZ-SP2

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_079557420.1 CDL62_RS10145 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>NCBI__GCF_002201795.1:WP_079557420.1
          Length = 419

 Score =  378 bits (971), Expect = e-109
 Identities = 199/416 (47%), Positives = 277/416 (66%), Gaps = 29/416 (6%)

Query: 6   IRDVDLKGKRVIMRVDFNVPVKDGV-VQDDTRIRAALPTIKYALEQGAKVILLSHLGRPK 64
           I + +  GK+ I+RVDFNVP  +   + DDTRIRAA+PTI+  L+ G   I++SHLGRPK
Sbjct: 4   IENYNFSGKKAIVRVDFNVPFNEKFEITDDTRIRAAMPTIQKILKDGGSAIIMSHLGRPK 63

Query: 65  GEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGET 124
           G+ +P+FSL  +   L++ +G +V F    VG EVK   E LK G++LLLEN RF+  E 
Sbjct: 64  GKVNPDFSLNHIKAHLAKTVGTDVIFAGDCVGSEVKAKAESLKPGQILLLENLRFYL-EE 122

Query: 125 KNDPEL-----------------------AKFWASLADIHVNDAFGTAHRAHASNVGIAQ 161
           +  P+L                       +K  ASLAD++VNDAFGTAHRAHAS   IA 
Sbjct: 123 EGKPKLPEGASDEETKVAKAEMKEKQKAFSKELASLADVYVNDAFGTAHRAHASTAVIAD 182

Query: 162 FIPS---VAGFLMEKEIKFLSKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIG 218
           +  +   + GFL+E E++ L KV   P++P+  ++GGAKVS KI +I NL++K D +++G
Sbjct: 183 YFDTDSKMFGFLIESEVQSLDKVVKEPKRPFTAIMGGAKVSSKITIIENLLDKVDNLILG 242

Query: 219 GAMMFTFLKALGKEVGSSRVEEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEK 278
           G M FTF+KA G +VG+S  E++ +DLAKE+ +KAKEKGV ++L  D V           
Sbjct: 243 GGMTFTFMKARGGKVGNSICEDEYLDLAKEIEKKAKEKGVNLLLASDVVAGDSFSNDANT 302

Query: 279 KVVRIDDGIPEGWMGLDIGPETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALA 338
           ++V  DD IPEGW GLD GP +++ F   + ++ T++WNGP+GVFE+D FA+G++ VA A
Sbjct: 303 QIVSADD-IPEGWEGLDAGPNSVKEFCHVIENSATILWNGPVGVFEMDTFAKGSRAVADA 361

Query: 339 IAALTEKGAITVVGGGDSAAAVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASI 394
           I A T+KGA +++GGGDS A +NKFGL D  S++ST GGA LE+LEGKELPGI +I
Sbjct: 362 IVAGTKKGAFSLIGGGDSVACINKFGLADGVSYISTAGGALLEYLEGKELPGIKAI 417


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: 679
Number of extensions: 38
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: 419
Length adjustment: 35
Effective length of query: 619
Effective length of database: 384
Effective search space:   237696
Effective search space used:   237696
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