GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garK in Arenitalea lutea P7-3-5

Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate WP_019386038.1 P735_RS0100530 glycerate kinase

Query= BRENDA::P23524
         (381 letters)



>NCBI__GCF_000283015.1:WP_019386038.1
          Length = 374

 Score =  298 bits (762), Expect = 2e-85
 Identities = 157/359 (43%), Positives = 227/359 (63%)

Query: 1   MKIVIAPDSYKESLSASEVAQAIEKGFREIFPDAQYVSVPVADGGEGTVEAMIAATQGAE 60
           MKIV+APD +KESL+  +   A E+G +E FP+AQ + +P+ADGG+GT++ +    QG  
Sbjct: 1   MKIVLAPDKFKESLTGMQFCAAAEEGIKETFPNAQIIKLPLADGGDGTIDVLEYHLQGKR 60

Query: 61  RHAWVTGPLGEKVNASWGISGDGKTAFIEMAAASGLELVPAEKRDPLVTTSRGTGELILQ 120
               V  PL   + +S+      +TAFIEMA ASG+ L+  E+++   TT+ GTGELI+ 
Sbjct: 61  IKIKVNDPLFRPIESSYLFMDTIETAFIEMAEASGMHLLKKEEQNCYFTTTLGTGELIVD 120

Query: 121 ALESGATNIIIGIGGSATNDGGAGMVQALGAKLCDANGNEIGFGGGSLNTLNDIDISGLD 180
           A++ GA  II+GIGGSATND G GM  ALG K  D NG ++   G +LN ++ I+   + 
Sbjct: 121 AIDKGAKTIILGIGGSATNDCGIGMATALGFKFEDENGKDLLPIGKNLNKIHAINTHKVL 180

Query: 181 PRLKDCVIRVACDVTNPLVGDNGASRIFGPQKGASEAMIVELDNNLSHYAEVIKKALHVD 240
             LK    +VACDVTNPL G  GA+ I+GPQKGASE  I  LD+ L + A + KK  ++D
Sbjct: 181 SGLKHIKFKVACDVTNPLYGKEGAAYIYGPQKGASETEIKNLDDGLKNIAMLFKKQFNID 240

Query: 241 VKDVPGAGAAGGMGAALMAFLGAELKSGIEIVTTALNLEEHIHDCTLVITGEGRIDSQSI 300
           V+ + G GAAGGMGA    FL A+LKSGI+++   +  ++ I +   ++TGEG++DSQ++
Sbjct: 241 VQKIKGTGAAGGMGAGTFTFLNADLKSGIDLIKDLIGFDDKIKEADWIVTGEGKLDSQTL 300

Query: 301 HGKVPIGVANVAKKYHKPVIGIAGSLTDDVGVVHQHGIDAVFSVLTSIGTLDEAFRGAY 359
            GK   GV   AKKY+ PV  + GS+T  +   +  GI  V +V+    +L++A +  Y
Sbjct: 301 SGKTISGVLESAKKYNIPVAALCGSVTLSIKQANDLGICYVGAVIKKANSLEDAMQNGY 359


Lambda     K      H
   0.315    0.135    0.385 

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: 418
Number of extensions: 20
Number of successful extensions: 2
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: 381
Length of database: 374
Length adjustment: 30
Effective length of query: 351
Effective length of database: 344
Effective search space:   120744
Effective search space used:   120744
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: 42 (22.0 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