GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Shewanella amazonensis SB2B

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 6938704 Sama_2807 phosphoribosylglycinamide formyltransferase 2 (RefSeq)

Query= SwissProt::P33221
         (392 letters)



>FitnessBrowser__SB2B:6938704
          Length = 392

 Score =  524 bits (1349), Expect = e-153
 Identities = 269/389 (69%), Positives = 313/389 (80%), Gaps = 1/389 (0%)

Query: 3   LLGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINML 62
           ++GT     ATR MLLGSGELGKEVAIE QRLGVEVIAVDRY +APAM VAHRSHVINML
Sbjct: 1   MIGTPYTQGATRAMLLGSGELGKEVAIELQRLGVEVIAVDRYPNAPAMQVAHRSHVINML 60

Query: 63  DGDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRLAA 122
           DG+AL+ ++  EKPH ++PEIEAIAT  L++LE EGL VVP ARAT+LTM+REGIRRLAA
Sbjct: 61  DGEALKALIASEKPHLVIPEIEAIATQTLVELEAEGLKVVPTARATRLTMDREGIRRLAA 120

Query: 123 EELQLPTSTYRFADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKYAQ 182
           E L LPTS Y F DS +  + A+   G PC+VKPVMSSSGKGQ+ IRS   + +AW YAQ
Sbjct: 121 ETLALPTSPYVFCDSLTELQAALKVTGIPCVVKPVMSSSGKGQSVIRSPGDVQKAWDYAQ 180

Query: 183 QGGRAGAGRVIVEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESWQPQQMSPL 242
            GGRAG GR+IVEG + FD+EITLLT+SAVDG+HFCAP+GHRQEDGDYRESWQPQ MS L
Sbjct: 181 SGGRAGEGRIIVEGFIDFDYEITLLTISAVDGIHFCAPIGHRQEDGDYRESWQPQAMSSL 240

Query: 243 ALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEFAL 302
           AL+RAQ IAR+VV  LGG+GLFGVELF+ GDEV FSEVSPRPHDTGMVTLISQDLSEFAL
Sbjct: 241 ALDRAQHIAREVVQNLGGFGLFGVELFIKGDEVYFSEVSPRPHDTGMVTLISQDLSEFAL 300

Query: 303 HVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAVG-ADLQIRLFGKPEIDGS 361
           HVRA LGLPVG I Q GP+ASAVIL +  S N+ +  +  A+   + Q+RLF KPEI G 
Sbjct: 301 HVRAILGLPVGTIVQRGPSASAVILVEGESSNIGYSGLAEALAQPNTQLRLFAKPEIHGR 360

Query: 362 RRLGVALATAESVVDAIERAKHAAGQVKV 390
           RRLGVALA   S+ +A++ A  +AG +KV
Sbjct: 361 RRLGVALARGTSIDEALQTALASAGCIKV 389


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: 472
Number of extensions: 18
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: 392
Length of database: 392
Length adjustment: 31
Effective length of query: 361
Effective length of database: 361
Effective search space:   130321
Effective search space used:   130321
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