GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Luteimonas huabeiensis HB2

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 WP_024891040.1 Z164_RS0112570 formate-dependent phosphoribosylglycinamide formyltransferase

Query= SwissProt::P33221
         (392 letters)



>NCBI__GCF_000559025.1:WP_024891040.1
          Length = 404

 Score =  472 bits (1214), Expect = e-138
 Identities = 258/398 (64%), Positives = 294/398 (73%), Gaps = 15/398 (3%)

Query: 1   MTLLGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVIN 60
           M  LGT L P+ATRV+LLGSGELGKEVAIE QR G EVIA DRYADAPAM VAHRSHV++
Sbjct: 1   MVRLGTPLSPSATRVLLLGSGELGKEVAIELQRFGAEVIAADRYADAPAMQVAHRSHVLD 60

Query: 61  MLDGDALRRVVELEKPHYIVPEIEAIATDMLIQLEEE------GLNVVPCARATKLTMNR 114
           MLDG A+R +V  E+PH IVPEIEAI T  L+ LE E         V+P ARA +LTM+R
Sbjct: 61  MLDGAAIRALVAHERPHLIVPEIEAIHTPTLVALEREFAEAGTATRVIPTARAARLTMDR 120

Query: 115 EGIRRLAAEELQLPTSTYRFADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQL 174
           EGIRRLAAE L LPTS YRF DS   +R AVA+IG PC+VKPVMSSSGKGQ+ +R A Q+
Sbjct: 121 EGIRRLAAETLGLPTSPYRFVDSLEDYRAAVAEIGLPCVVKPVMSSSGKGQSLVREAAQV 180

Query: 175 AQAWKYAQQGGRAGAGRVIVEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESW 234
             AW +AQ GGRAGAGRVIVEG V FD+EITLLTV    G  FCAP+GH Q DGDYRESW
Sbjct: 181 DGAWDHAQTGGRAGAGRVIVEGFVDFDYEITLLTVRHAGGTAFCAPIGHLQRDGDYRESW 240

Query: 235 QPQQMSPLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLIS 294
           QPQ MSPLAL R+QEIAR +   LGG+G+FGVELFV GDEV FSEVSPRPHDTG+VTL S
Sbjct: 241 QPQPMSPLALARSQEIARAITDDLGGWGVFGVELFVKGDEVWFSEVSPRPHDTGLVTLAS 300

Query: 295 QDLSEFALHVRAFLGLPV-----GGIRQYGPAASAVILPQLTSQNV-TFDNVQNAVGA-D 347
           Q+LSEFALH RA LGLPV     G +   GPAAS  +L Q     V  F NV+ A+ A  
Sbjct: 301 QELSEFALHARAILGLPVPADADGTVPLLGPAASCALLAQ--GHGVPAFANVEAALRAPG 358

Query: 348 LQIRLFGKPEIDGSRRLGVALATAESVVDAIERAKHAA 385
             +RLFGKP ++G RR+GV LA A+ V  A   A+ AA
Sbjct: 359 TALRLFGKPRVEGQRRVGVTLARAQDVEAARATAREAA 396


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: 514
Number of extensions: 22
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: 392
Length of database: 404
Length adjustment: 31
Effective length of query: 361
Effective length of database: 373
Effective search space:   134653
Effective search space used:   134653
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 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