GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Herbaspirillum seropedicae SmR1

Align Formate-dependent phosphoribosylglycinamide formyltransferase; 5'-phosphoribosylglycinamide transformylase 2; Formate-dependent GAR transformylase; GAR transformylase 2; GART 2; Non-folate glycinamide ribonucleotide transformylase; Phosphoribosylglycinamide formyltransferase 2; EC 2.1.2.- (characterized)
to candidate HSERO_RS11090 HSERO_RS11090 phosphoribosylglycinamide formyltransferase

Query= SwissProt::P33221
         (392 letters)



>FitnessBrowser__HerbieS:HSERO_RS11090
          Length = 403

 Score =  435 bits (1118), Expect = e-126
 Identities = 242/395 (61%), Positives = 283/395 (71%), Gaps = 8/395 (2%)

Query: 2   TLLGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINM 61
           T LGT L  +AT+VMLLGSGELGKEV I  QRLGVEVIAVDRY +AP   VAHR+HVINM
Sbjct: 5   TRLGTPLSSSATKVMLLGSGELGKEVIIALQRLGVEVIAVDRYENAPGHQVAHRAHVINM 64

Query: 62  LDGDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEGL-NVVPCARATKLTMNREGIRRL 120
            DG AL  ++E EKP  IVPEIEAIAT+ L++LEE GL  V+P ARA  LTMNREGIRRL
Sbjct: 65  TDGAALAALIEQEKPDLIVPEIEAIATETLVKLEEAGLARVIPTARAAWLTMNREGIRRL 124

Query: 121 AAEELQLPTSTYRFADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKY 180
           A E L L TS YRFADS    + A+  IGYPC++KPVMSSSGKGQ+ I   +++  AW Y
Sbjct: 125 AGETLGLATSPYRFADSLEELKAAIDQIGYPCVIKPVMSSSGKGQSKIDGPDEIESAWNY 184

Query: 181 AQQGGRAGAGRVIVEGVVKFDFEITLLTVSAVDG-----VHFCAPVGHRQEDGDYRESWQ 235
           A  GGR  AGRVIVEG + FD+EITLLTV +++        FC P+GH Q  GDY ESWQ
Sbjct: 185 AAAGGRVDAGRVIVEGFIDFDYEITLLTVRSLNENGDTVTSFCDPIGHVQVKGDYVESWQ 244

Query: 236 PQQMSPLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQ 295
           P  M   ALE+A++IARKV   LGG GLFGVELFV GD V FSEVSPRPHDTGMVT++SQ
Sbjct: 245 PHPMPGAALEKARDIARKVTENLGGLGLFGVELFVKGDMVWFSEVSPRPHDTGMVTMVSQ 304

Query: 296 DLSEFALHVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAVG-ADLQIRLFG 354
             SEF LH +A LGLPV    +  P ASAVI  Q  ++ + FD V  A+     +IRLFG
Sbjct: 305 VQSEFELHAKAILGLPVNTALR-TPGASAVIYGQHEARGIAFDGVAEALRIPGAEIRLFG 363

Query: 355 KPEIDGSRRLGVALATAESVVDAIERAKHAAGQVK 389
           KPE    RR+GVALA+A++V  A  RAK AA +VK
Sbjct: 364 KPESFARRRMGVALASADNVETARIRAKQAAAKVK 398


Lambda     K      H
   0.320    0.136    0.390 

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: 465
Number of extensions: 23
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: 392
Length of database: 403
Length adjustment: 31
Effective length of query: 361
Effective length of database: 372
Effective search space:   134292
Effective search space used:   134292
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 Sep 17 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