GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Shewanella loihica PV-4

Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate 5207773 Shew_0294 alanine--glyoxylate transaminase (RefSeq)

Query= BRENDA::P21549
         (392 letters)



>FitnessBrowser__PV4:5207773
          Length = 380

 Score =  274 bits (700), Expect = 4e-78
 Identities = 154/383 (40%), Positives = 220/383 (57%), Gaps = 7/383 (1%)

Query: 7   LVTPPKALLKPLSIPNQLLLGPGPSNLPPRIMAAGGLQMIGSMSKDMYQIMDEIKEGIQY 66
           ++  PK  + P + P ++L+GPGPS++ P ++AA     IG +      +MDE+K  IQY
Sbjct: 1   MLAAPK--VTPFNPPRRVLMGPGPSDVYPEVLAAQARPTIGHLDPLFVGMMDELKSLIQY 58

Query: 67  VFQTRNPLTLVISGSGHCALEAALVNVLEPGDSFLVGANGIWGQRAVDIGERIGARVHPM 126
            FQT N +TL +S  G   +E   VN++EPG+  +V  NG++G+R     ER+GA    +
Sbjct: 59  AFQTENAMTLAVSAPGSAGMETCFVNLVEPGEKVIVCRNGVFGERMRQNVERVGATAVVV 118

Query: 127 TKDPGGHYTLQEVEEGLAQHKPV-LLFLTHGESSTGVLQPLDGFGELCHRYKCLLLVDSV 185
             + G   +L +VE  L  H     L   H E+STG L    G  +L   + CL +VD+V
Sbjct: 119 DNEWGTPVSLSDVEAALKAHPDAKFLAFVHAETSTGALSDAKGLCQLAKAHDCLSIVDAV 178

Query: 186 ASLGGTPLYMDRQGIDILYSGSQKALNAPPGTSLISFSDKAKKKMYSRKTKPFSFYLDIK 245
            SLGG  L +D  GID +YSGSQK L+  PG S +SFS  A +K+ +RKT   S++LD  
Sbjct: 179 TSLGGVELRVDEWGIDAIYSGSQKCLSCVPGLSPVSFSPAAVEKLKARKTPVQSWFLDQS 238

Query: 246 WLANFWGCDD---QPRMYHHTIPVISLYSLRESLALIAEQGLENSWRQHREAAAYLHGRL 302
            +  +W  D      R YHHT PV +LY+L ESL L+AE+GLEN+W +H    A L   L
Sbjct: 239 LVMGYWSGDQGAGGKRSYHHTAPVNALYALHESLRLLAEEGLENAWARHHSMHALLRDGL 298

Query: 303 QALGLQLFVKDPALRLPTVTTVAVPAGYDWRDIVSYVIDHFDIEIMGGLGPSTGKVLRIG 362
           + LGL+ FV +   RLP +  V +P G D   +   +++++++EI  GLG   GK  RIG
Sbjct: 299 ENLGLK-FVVEEGSRLPQLNAVYIPEGVDDGAVRKQLLENYNLEIGAGLGALAGKAWRIG 357

Query: 363 LLGCNATRENVDRVTEALRAALQ 385
           L+G  A RENV     AL   L+
Sbjct: 358 LMGFGARRENVALCLRALEEVLR 380


Lambda     K      H
   0.320    0.138    0.421 

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: 378
Number of extensions: 17
Number of successful extensions: 4
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: 392
Length of database: 380
Length adjustment: 30
Effective length of query: 362
Effective length of database: 350
Effective search space:   126700
Effective search space used:   126700
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: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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