Alignments for a candidate for pgmA in Leptospirillum ferrooxidans C2-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Leptospirillum ferrooxidans C2-3

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_014449979.1 LFE_RS09370 alpha-D-glucose phosphate-specific phosphoglucomutase

Query= BRENDA::I6Y2G3
         (547 letters)



>NCBI__GCF_000284315.1:WP_014449979.1
          Length = 547

 Score =  614 bits (1584), Expect = e-180
 Identities = 318/549 (57%), Positives = 386/549 (70%), Gaps = 7/549 (1%)

Query: 1   MVANPRAGQPAQPEDLVDLPHLVTAYYSIEPDPDDLAQQVAFGTSGHRGSALTGTFNELH 60
           M  NP AG+PA P+ LVD+  LVTAY++  PDP   +++V+FGTSGHRGS+ + +FNE H
Sbjct: 1   MPINPLAGKPASPDVLVDVSKLVTAYFTEMPDPRVPSERVSFGTSGHRGSSFSRSFNEEH 60

Query: 61  ILAITQAIVEYRAAQGTTGPLFIGRDTHGLSEPAWVSALEVLAANQVVAVVDSRDRYTPT 120
           IL ITQAI  YR +Q   GPL++G DTH LS PA V+ALEVL+AN +   +   D +TPT
Sbjct: 61  ILCITQAICLYRKSQKIDGPLYLGIDTHALSVPAMVTALEVLSANDIDVYLAYNDEFTPT 120

Query: 121 PAISHAILTYNRGRTEALADGIVVTPSHNPPSDGGIKYNPPNGGPADTAATTAIAKRANE 180
           P ISHAILTYN  R   LADGIV+TPSHNPP DGG KYNPPNGGPADTA T+ I  +AN 
Sbjct: 121 PVISHAILTYNANRKTGLADGIVITPSHNPPHDGGFKYNPPNGGPADTAITSWIENKANG 180

Query: 181 ILL-ARSMVKRLPLARALR--TAQRHDYLGHYVDDLPNVVDIAAIREAGVRIGADPLGGA 237
            L      +KR+  ARAL+  T  RHD+LG YV DL NVVD+  IR + +R+G DPLGGA
Sbjct: 181 FLEDCLQGIKRISYARALKSPTTHRHDFLGSYVGDLGNVVDMEMIRSSKIRMGVDPLGGA 240

Query: 238 SVDYWGEIAHRHGLDLTVVNPLVDATWRFMTLDTDGKIRMDCSSPDAMAGLIRTMFGNRE 297
            V YW  IA ++ LDLT VN  VD T+RFMTLD DG+IRMD SSP AM  L+      ++
Sbjct: 241 GVHYWNRIAEQYNLDLTCVNQTVDPTFRFMTLDWDGQIRMDPSSPYAMESLVAM----KD 296

Query: 298 RYQIATGNDADADRHGIVTPDEGLLNPNHYLAVAIEYLYTHRPSWPAGIAVGKTVVSSSI 357
           R+ IA   D D DRHGIVT   GL+ PNHYL+V + YL+THRP W A   VGKT+VSS +
Sbjct: 297 RFDIAFAADTDHDRHGIVTKSSGLMAPNHYLSVMVSYLFTHRPKWAAKARVGKTLVSSKM 356

Query: 358 IDRVVAGIGRQLVEVPVGFKWFVDGLIGATLGFGGEESAGASFLRRDGSVWTTDKDGIIM 417
           ID V   +GR L EVPVGFK+FVDGLI  +LGF GEESAGASFLR DG VW+TDKDGII 
Sbjct: 357 IDAVAKDLGRDLYEVPVGFKYFVDGLIDGSLGFTGEESAGASFLRIDGGVWSTDKDGIIP 416

Query: 418 ALLAAEILAVTGATPSQRYHALAGEYGGPCYARIDAPADREQKARLARLSADQVSATELA 477
            LL+AE+ A T   P + Y  L   +G P Y RIDAPA   QK+ L  L+ ++V + ELA
Sbjct: 417 GLLSAEMTARTQMDPGESYRHLCERFGNPAYRRIDAPATDWQKSLLKNLTPEKVRSGELA 476

Query: 478 GEPITAKLTTAPGNGAALGGLKVTTANAWFAARPSGTEDVYKIYAESFRGPQHLVEVQQT 537
           GE I   LT APGN  ++GGLKV T + WFAARPSGTE +YKIYAESF G +HL  +   
Sbjct: 477 GEKILECLTKAPGNNQSIGGLKVVTKSGWFAARPSGTESIYKIYAESFGGEEHLGRILSE 536

Query: 538 AREVVDRVI 546
           A+EVV++ +
Sbjct: 537 AQEVVNKAL 545


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: 927
Number of extensions: 34
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: 547
Length adjustment: 36
Effective length of query: 511
Effective length of database: 511
Effective search space:   261121
Effective search space used:   261121
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_014449979.1 LFE_RS09370 (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.7725.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     3e-262  856.7   0.0   3.4e-262  856.6   0.0    1.0  1  lcl|NCBI__GCF_000284315.1:WP_014449979.1  LFE_RS09370 alpha-D-glucose phos


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000284315.1:WP_014449979.1  LFE_RS09370 alpha-D-glucose phosphate-specific phosphoglucomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  856.6   0.0  3.4e-262  3.4e-262       1     545 [.       1     545 [.       1     546 [. 1.00

  Alignments for each domain:
  == domain 1  score: 856.6 bits;  conditional E-value: 3.4e-262
                                 TIGR01132   1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavv 69 
                                               m inp+aG++a ++ l+dv+klv++y++  pd+  ++++v+fGtsGhrGs+   +fne+hil i+qa+ 
  lcl|NCBI__GCF_000284315.1:WP_014449979.1   1 MPINPLAGKPASPDVLVDVSKLVTAYFTEMPDPRVPSERVSFGTSGHRGSSFSRSFNEEHILCITQAIC 69 
                                               679****************************************************************** PP

                                 TIGR01132  70 evraaqGitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkeal 138
                                                +r+ q i Gply+G dthals pa+v++levl an+++v +  n+ +tptp +shailtyn  +k +l
  lcl|NCBI__GCF_000284315.1:WP_014449979.1  70 LYRKSQKIDGPLYLGIDTHALSVPAMVTALEVLSANDIDVYLAYNDEFTPTPVISHAILTYNANRKTGL 138
                                               ********************************************************************* PP

                                 TIGR01132 139 adGivitpshnppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekd 207
                                               adGivitpshnpp+dGG+kynppnGGpa+t++t +ie++an +l+d l+g+kr+++++alks t++++d
  lcl|NCBI__GCF_000284315.1:WP_014449979.1 139 ADGIVITPSHNPPHDGGFKYNPPNGGPADTAITSWIENKANGFLEDCLQGIKRISYARALKSPTTHRHD 207
                                               ********************************************************************* PP

                                 TIGR01132 208 lvkpyvddladvvdlaairkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdG 276
                                               ++  yv dl +vvd+++ir++++r+GvdplGGagv+yw++iae+ynldlt vn++vd+tfrfmtld+dG
  lcl|NCBI__GCF_000284315.1:WP_014449979.1 208 FLGSYVGDLGNVVDMEMIRSSKIRMGVDPLGGAGVHYWNRIAEQYNLDLTCVNQTVDPTFRFMTLDWDG 276
                                               ********************************************************************* PP

                                 TIGR01132 277 kirmdcsspyamagllklkdkydlafgndadadrhGivtpdkGllnpnhylavaieylykhrqqwaaev 345
                                               +irmd sspyam +l+++kd++d+af+ d+d drhGivt ++Gl+ pnhyl+v ++yl++hr++waa+ 
  lcl|NCBI__GCF_000284315.1:WP_014449979.1 277 QIRMDPSSPYAMESLVAMKDRFDIAFAADTDHDRHGIVTKSSGLMAPNHYLSVMVSYLFTHRPKWAAKA 345
                                               ********************************************************************* PP

                                 TIGR01132 346 avGktlvssalidrvvadlgrklvevpvGfkwfvdGlldgslGfGGeesaGasflrkdGtvwstdkdGi 414
                                                vGktlvss +id v+ dlgr+l+evpvGfk+fvdGl+dgslGf GeesaGasflr dG vwstdkdGi
  lcl|NCBI__GCF_000284315.1:WP_014449979.1 346 RVGKTLVSSKMIDAVAKDLGRDLYEVPVGFKYFVDGLIDGSLGFTGEESAGASFLRIDGGVWSTDKDGI 414
                                               ********************************************************************* PP

                                 TIGR01132 415 ilallaaeitavtGknpqqrydelaakyGdpiyaridaaatsaqkarlkklspdevsattlaGdaitak 483
                                               i  ll+ae+ta t  +p++ y +l++++G+p+y+rida+at  qk+ lk+l+p++v + +laG+ i   
  lcl|NCBI__GCF_000284315.1:WP_014449979.1 415 IPGLLSAEMTARTQMDPGESYRHLCERFGNPAYRRIDAPATDWQKSLLKNLTPEKVRSGELAGEKILEC 483
                                               ********************************************************************* PP

                                 TIGR01132 484 ltkapGngaaiGGlkvttdegwfaarpsGtedvykiyaesfkgeehlkeiekeaeeivdevl 545
                                               ltkapGn+ +iGGlkv+t+ gwfaarpsGte +ykiyaesf geehl +i +ea+e+v+++l
  lcl|NCBI__GCF_000284315.1:WP_014449979.1 484 LTKAPGNNQSIGGLKVVTKSGWFAARPSGTESIYKIYAESFGGEEHLGRILSEAQEVVNKAL 545
                                               ***********************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (547 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 12.75
//
[ok]

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

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

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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:

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 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