GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruG in Chromobacterium vaccinii MWU205

Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate WP_046157872.1 VL52_RS15515 arginine N-succinyltransferase

Query= BRENDA::P80358
         (340 letters)



>NCBI__GCF_000971335.1:WP_046157872.1
          Length = 348

 Score =  360 bits (925), Expect = e-104
 Identities = 186/344 (54%), Positives = 239/344 (69%), Gaps = 6/344 (1%)

Query: 1   MIVRPVTSADLPALIELARST---GTGLTTLPANEQRLQHRVSWAEKAFRGEAERGDADY 57
           M +RPV   DLP L+ELARS    G GLT+LP NE RLQ R++ +  +F GE +R D  Y
Sbjct: 2   MFIRPVEHKDLPGLMELARSAASGGVGLTSLPINEDRLQKRIARSVLSFSGELDRADHGY 61

Query: 58  LFVLED-DAGKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTG 116
           +FVLED + GKV GI A+  AVGL+EPWYNYR+G  V AS+EL ++    TLFL+ND TG
Sbjct: 62  VFVLEDSENGKVAGICAVEAAVGLKEPWYNYRIGTIVHASEELGVYSRHETLFLSNDHTG 121

Query: 117 NSELCSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWES 176
            SELC+L+LH D+R   NG LLS++RFLF+A+F  LFG  ++AEMRG+SDE GRSPFWE+
Sbjct: 122 YSELCTLYLHPDYRVKRNGGLLSKSRFLFLAQFPQLFGKMVVAEMRGVSDENGRSPFWEA 181

Query: 177 LGRHFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAM 236
           LGRHFF ++F++ADYLTG+G KAF+AELMPK P+Y  FL  EA+ VIG  H  T PA+AM
Sbjct: 182 LGRHFFSIDFAEADYLTGIGQKAFVAELMPKHPVYVDFLEPEAQAVIGLTHEATRPAVAM 241

Query: 237 LKAEGFSYQGYVDIFDAGPAIEAETDKIRAIAESQNLVLAV--GTPGDDAEPYLIHNRKR 294
           L++EGF Y+GYVDIFDAGP ++A T  IRA+ ESQ L   V    P  D E YL+ N   
Sbjct: 242 LESEGFRYEGYVDIFDAGPTVQAYTGDIRAVKESQRLPARVVDPLPDGDKECYLVCNDAL 301

Query: 295 EDCRITAAPARAAAGTLVVDPLTAKRLRLSAGASVRAVPLSAQK 338
           +D R   A +    G   + P  A+ L++  G  VR V L+ ++
Sbjct: 302 QDYRAVLAESVRPQGEFCLTPELARALKIKDGDHVRCVTLTPKE 345


Lambda     K      H
   0.320    0.136    0.398 

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: 372
Number of extensions: 7
Number of successful extensions: 3
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: 340
Length of database: 348
Length adjustment: 29
Effective length of query: 311
Effective length of database: 319
Effective search space:    99209
Effective search space used:    99209
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: 49 (23.5 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