Alignments for a candidate for pgmA in Rhodococcus qingshengii djl-6-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Rhodococcus qingshengii djl-6-2

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_047271638.1 C1M55_RS11860 alpha-D-glucose phosphate-specific phosphoglucomutase

Query= BRENDA::I6Y2G3
         (547 letters)



>NCBI__GCF_002893965.1:WP_047271638.1
          Length = 545

 Score =  796 bits (2056), Expect = 0.0
 Identities = 398/546 (72%), Positives = 455/546 (83%), Gaps = 5/546 (0%)

Query: 2   VANPRAGQPAQPEDLVDLPHLVTAYYSIEPDPDDLAQQVAFGTSGHRGSALTGTFNELHI 61
           +A+ RAGQ A PEDL+++PHLVTAYY+  PDP++  QQV FGTSGHRGS+L   FNE HI
Sbjct: 1   MAHERAGQVALPEDLINVPHLVTAYYTRTPDPENPMQQVLFGTSGHRGSSLDSAFNEAHI 60

Query: 62  LAITQAIVEYRAAQGTTGPLFIGRDTHGLSEPAWVSALEVLAANQVVAVVDSRDRYTPTP 121
           LA TQAIVEYRA+QG  GPLFIGRDTH LSEPAW+SALEVL AN VV +VDSRD YTPTP
Sbjct: 61  LATTQAIVEYRASQGIDGPLFIGRDTHALSEPAWLSALEVLVANDVVVLVDSRDAYTPTP 120

Query: 122 AISHAILTYNRGRTEALADGIVVTPSHNPPSDGGIKYNPPNGGPADTAATTAIAKRANEI 181
           A+SHAIL YN    EA ADGIVVTPSHNPP DGG KYNPP+GGPADT AT+ IA RANE+
Sbjct: 121 AVSHAILRYNSTGPEAKADGIVVTPSHNPPCDGGFKYNPPHGGPADTDATSVIADRANEL 180

Query: 182 LL-ARSMVKRLPLARALRTAQRHDYLGHYVDDLPNVVDIAAIREAGVRIGADPLGGASVD 240
           L    S V+R+  A+AL   +R+D+L +YV+DLP+V+++ AIR+AG+RIGADPLGGASVD
Sbjct: 181 LRKGLSGVRRVTAAQALDRVERYDFLRYYVEDLPSVLNLDAIRDAGIRIGADPLGGASVD 240

Query: 241 YWGEIAHRHGLDLTVVNPLVDATWRFMTLDTDGKIRMDCSSPDAMAGLIRTMFGNRERYQ 300
           YWG IA  H LDL VVNPLVD TWRFMTLDTDGKIRMDCSSPDAMA LI    G R+RY 
Sbjct: 241 YWGAIAETHRLDLEVVNPLVDPTWRFMTLDTDGKIRMDCSSPDAMASLI----GIRDRYD 296

Query: 301 IATGNDADADRHGIVTPDEGLLNPNHYLAVAIEYLYTHRPSWPAGIAVGKTVVSSSIIDR 360
           IATGNDAD+DRHGIVTPD GL+NPNHYLAVAIEYL+ +RP W A   VGKT+VSSS+IDR
Sbjct: 297 IATGNDADSDRHGIVTPDGGLMNPNHYLAVAIEYLFANRPGWGADTKVGKTLVSSSMIDR 356

Query: 361 VVAGIGRQLVEVPVGFKWFVDGLIGATLGFGGEESAGASFLRRDGSVWTTDKDGIIMALL 420
           VV+ +GR+L+EVPVGFKWFV GL+  ++GFGGEESAGASFLR DGSVWTTDKDGII+ALL
Sbjct: 357 VVSSLGRELLEVPVGFKWFVPGLLDGSVGFGGEESAGASFLRHDGSVWTTDKDGIILALL 416

Query: 421 AAEILAVTGATPSQRYHALAGEYGGPCYARIDAPADREQKARLARLSADQVSATELAGEP 480
           A+EI AVTG +PS  Y ALA ++G P YARIDAPA R QKA LA+LS DQVSATELAGEP
Sbjct: 417 ASEITAVTGESPSAHYAALAEKFGSPAYARIDAPATRAQKAVLAKLSPDQVSATELAGEP 476

Query: 481 ITAKLTTAPGNGAALGGLKVTTANAWFAARPSGTEDVYKIYAESFRGPQHLVEVQQTARE 540
           ITA LT APGNGAA+GGLKVTT NAWFAARPSGTEDVYKIYAES +G  HL +VQ  A++
Sbjct: 477 ITATLTAAPGNGAAIGGLKVTTENAWFAARPSGTEDVYKIYAESMKGADHLAQVQAAAKD 536

Query: 541 VVDRVI 546
           +V  V+
Sbjct: 537 LVSGVL 542


Lambda     K      H
   0.318    0.135    0.401 

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: 1112
Number of extensions: 43
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: 547
Length of database: 545
Length adjustment: 35
Effective length of query: 512
Effective length of database: 510
Effective search space:   261120
Effective search space used:   261120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_047271638.1 C1M55_RS11860 (alpha-D-glucose phosphate-specific phosphoglucomutase)
to HMM TIGR01132 (pgm: phosphoglucomutase, alpha-D-glucose phosphate-specific (EC 5.4.2.2))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01132.hmm
# target sequence database:        /tmp/gapView.273278.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01132  [M=546]
Accession:   TIGR01132
Description: pgm: phosphoglucomutase, alpha-D-glucose phosphate-specific
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.3e-290  948.6   0.1   4.9e-290  948.5   0.1    1.0  1  NCBI__GCF_002893965.1:WP_047271638.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002893965.1:WP_047271638.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  948.5   0.1  4.9e-290  4.9e-290       3     546 .]       2     543 ..       1     543 [. 1.00

  Alignments for each domain:
  == domain 1  score: 948.5 bits;  conditional E-value: 4.9e-290
                             TIGR01132   3 inpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevraaq 75 
                                           +++raGq a +edl++v++lv++yy+  pd+en+ q+v fGtsGhrGs+l ++fneahila +qa+ve+ra q
  NCBI__GCF_002893965.1:WP_047271638.1   2 AHERAGQVALPEDLINVPHLVTAYYTRTPDPENPMQQVLFGTSGHRGSSLDSAFNEAHILATTQAIVEYRASQ 74 
                                           699********************************************************************** PP

                             TIGR01132  76 GitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkealadGivitpsh 148
                                           Gi Gpl+iG+dthalsepa+ s+levl+an+v+v+v++++ ytptpavshail yn    ea+adGiv+tpsh
  NCBI__GCF_002893965.1:WP_047271638.1  75 GIDGPLFIGRDTHALSEPAWLSALEVLVANDVVVLVDSRDAYTPTPAVSHAILRYNSTGPEAKADGIVVTPSH 147
                                           ************************************************************************* PP

                             TIGR01132 149 nppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladvvd 221
                                           npp dGG+kynpp+GGpa+t++t +i+dranell+++l+gv+r++ ++al    v++ d+++ yv+dl+ v++
  NCBI__GCF_002893965.1:WP_047271638.1 148 NPPCDGGFKYNPPHGGPADTDATSVIADRANELLRKGLSGVRRVTAAQALD--RVERYDFLRYYVEDLPSVLN 218
                                           *************************************************98..9******************* PP

                             TIGR01132 222 laairkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagllkl 294
                                           l+air+ag+r+G+dplGGa+vdyw  iae++ ldl +vn+ vd+t+rfmtld+dGkirmdcssp+ama+l+ +
  NCBI__GCF_002893965.1:WP_047271638.1 219 LDAIRDAGIRIGADPLGGASVDYWGAIAETHRLDLEVVNPLVDPTWRFMTLDTDGKIRMDCSSPDAMASLIGI 291
                                           ************************************************************************* PP

                             TIGR01132 295 kdkydlafgndadadrhGivtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlgrk 367
                                           +d+yd+a+gndad+drhGivtpd Gl+npnhylavaieyl+ +r++w+a++ vGktlvss++idrvv++lgr+
  NCBI__GCF_002893965.1:WP_047271638.1 292 RDRYDIATGNDADSDRHGIVTPDGGLMNPNHYLAVAIEYLFANRPGWGADTKVGKTLVSSSMIDRVVSSLGRE 364
                                           ************************************************************************* PP

                             TIGR01132 368 lvevpvGfkwfvdGlldgslGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydelaa 440
                                           l+evpvGfkwfv Glldgs+GfGGeesaGasflr+dG+vw+tdkdGiilalla+eitavtG++p+ +y +la+
  NCBI__GCF_002893965.1:WP_047271638.1 365 LLEVPVGFKWFVPGLLDGSVGFGGEESAGASFLRHDGSVWTTDKDGIILALLASEITAVTGESPSAHYAALAE 437
                                           ************************************************************************* PP

                             TIGR01132 441 kyGdpiyaridaaatsaqkarlkklspdevsattlaGdaitakltkapGngaaiGGlkvttdegwfaarpsGt 513
                                           k+G+p+yarida+at+aqka+l+klspd+vsat+laG++ita lt+apGngaaiGGlkvtt+++wfaarpsGt
  NCBI__GCF_002893965.1:WP_047271638.1 438 KFGSPAYARIDAPATRAQKAVLAKLSPDQVSATELAGEPITATLTAAPGNGAAIGGLKVTTENAWFAARPSGT 510
                                           ************************************************************************* PP

                             TIGR01132 514 edvykiyaesfkgeehlkeiekeaeeivdevlk 546
                                           edvykiyaes+kg++hl +++  a+++v+ vlk
  NCBI__GCF_002893965.1:WP_047271638.1 511 EDVYKIYAESMKGADHLAQVQAAAKDLVSGVLK 543
                                           *****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (545 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 19.52
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources