GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argE in Pontibacter ramchanderi LP43

Align Predicted argE by GapMind curators (no experimental data)
to candidate WP_101444052.1 BD749_RS08970 amidohydrolase

Query= predicted:W3Y6L2
         (394 letters)



>NCBI__GCF_002846395.1:WP_101444052.1
          Length = 399

 Score =  238 bits (608), Expect = 2e-67
 Identities = 150/400 (37%), Positives = 210/400 (52%), Gaps = 9/400 (2%)

Query: 1   MHTLQDLIKQYASQYKEQVVAWRRHIHSHPELSGEEKETSAFIQSVLTDLGIPFKADVYK 60
           M+ L   IK+ A  Y    V  RRHIH+HPELS EE  T+A+++ VL   G+     +  
Sbjct: 1   MNQLAQKIKELARAYTHDTVGIRRHIHAHPELSFEEHNTAAYVEQVLQSYGLE-TTRMAA 59

Query: 61  YAVIGEIKGAF-DGPVVGLRADMDALPITEVTGLPFTSENPGVMHACGHDSHMAILLGAA 119
             V+  IKG   +   + LRAD+DALPITE   + + S+N GVMHACGHD H A LLGAA
Sbjct: 60  TGVVALIKGRNPESKTIALRADLDALPITEQNSVDYKSKNEGVMHACGHDVHTASLLGAA 119

Query: 120 AILQSVKDQLHGTVKLVIQPAEEEALIKGAQGIVDSGVLDDVDE--IYGLHVWPQLPVGT 177
            ILQ +  +  GTVKLV QP EE+    GA  ++  GVL       I G HV+P LP G 
Sbjct: 120 RILQDLHHEFEGTVKLVFQPGEEK-FPGGASVMIKEGVLQQPAPAGIIGQHVFPMLPAGK 178

Query: 178 VGLKKGNLMAASDRFLVHIKGKATHGAEPHNGIDAIVAAANWIVNVESMVARETNPMDNL 237
           VG + G  MA++D   + +KGK  H A P   +D ++  ++ IV ++ +V+R  +P    
Sbjct: 179 VGFRSGMYMASADEIYITVKGKGGHAALPELNVDPVLITSHLIVALQQVVSRHASPKVPT 238

Query: 238 VCTIGVFNSGDRYNVGSGDAYLEGTCRTYDPAKRDYIERRLGESLKALDMMFGTTSTLEY 297
           V + G   +    NV   +  +EGT RT D   R    RR+    + L    G +  ++ 
Sbjct: 239 VLSFGKVEALGATNVIPNEVKVEGTFRTMDEVWRKEAHRRIRLLAEGLCESMGGSCDIDI 298

Query: 298 RRGHGATINDADAIDYVTHIVKTYLGKDAVVHPEFPSMAAEDFSAYLNKIKGAFLWLGTG 357
           + G+    ND D           YLG ++VV  +   M AEDF+ Y  ++   F  LGT 
Sbjct: 299 KFGYPFLKNDPDLTGRAREAAALYLGAESVVDLDL-WMGAEDFAYYSQEVAACFYRLGTR 357

Query: 358 FEG---NPALHNAAFTIDESILEPGITMMAGIAAELLQEK 394
            +       +H   F IDE+ LE GI +MA IA + L+ K
Sbjct: 358 NDERGITSGVHTPTFDIDEAALETGIGLMAWIAVQELEAK 397


Lambda     K      H
   0.318    0.136    0.401 

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: 405
Number of extensions: 15
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: 394
Length of database: 399
Length adjustment: 31
Effective length of query: 363
Effective length of database: 368
Effective search space:   133584
Effective search space used:   133584
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 Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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