Alignments for a candidate for pgmA in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Caulobacter crescentus NA1000

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate CCNA_00083 CCNA_00083 phosphoglucomutase/phosphomannomutase

Query= BRENDA::I6Y2G3
         (547 letters)



>FitnessBrowser__Caulo:CCNA_00083
          Length = 546

 Score =  739 bits (1909), Expect = 0.0
 Identities = 381/541 (70%), Positives = 432/541 (79%), Gaps = 9/541 (1%)

Query: 6   RAGQPAQPEDLVDLPHLVTAYYSIEPDPDDLAQQVAFGTSGHRGSALTGTFNELHILAIT 65
           RAG  A PEDLVDL  L+ AY+ I+PD  + AQ+V FGTSGHRGS+L G FNE HILA+T
Sbjct: 5   RAGLRALPEDLVDLDALIGAYFEIKPDVSNPAQKVVFGTSGHRGSSLDGAFNEAHILAVT 64

Query: 66  QAIVEYRAAQGTTGPLFIGRDTHGLSEPAWVSALEVLAANQVVAVVDSRDRYTPTPAISH 125
           QAIVEYRAAQG TGPLF+GRDTHGLSEPAW S LEVLAAN V A+VDSRD +TPTPA+SH
Sbjct: 65  QAIVEYRAAQGVTGPLFVGRDTHGLSEPAWRSVLEVLAANGVEALVDSRDGFTPTPAVSH 124

Query: 126 AILTYNR--GRTEALADGIVVTPSHNPPSDGGIKYNPPNGGPADTAATTAIAKRANEILL 183
           AILT+NR  GR    ADG+++TPSHNPP DGGIKYNPP+GGPA + AT+AIA RANE LL
Sbjct: 125 AILTHNRQGGRQ---ADGLLLTPSHNPPRDGGIKYNPPSGGPAGSDATSAIAARANE-LL 180

Query: 184 ARSM--VKRLPLARALRTAQRHDYLGHYVDDLPNVVDIAAIREAGVRIGADPLGGASVDY 241
           A+ +  VKR+P   A +    +D+LG YVDDLP V+DIAAIR A VRIGADPLGGA+V Y
Sbjct: 181 AQGLAGVKRVPFETARKAVGDYDFLGRYVDDLPAVIDIAAIRAAKVRIGADPLGGAAVAY 240

Query: 242 WGEIAHRHGLDLTVVNPLVDATWRFMTLDTDGKIRMDCSSPDAMAGLIRTMFGNRERYQI 301
           WG IA RH LDLTVVN  VD  W FM LDTDGKIRMDCSS  AMA LI  M G    Y +
Sbjct: 241 WGAIAERHALDLTVVNDAVDPRWAFMPLDTDGKIRMDCSSSSAMANLIGIMKGGAA-YDV 299

Query: 302 ATGNDADADRHGIVTPDEGLLNPNHYLAVAIEYLYTHRPSWPAGIAVGKTVVSSSIIDRV 361
           ATGNDADADRHGIVTPD GL+NPNHYLA AI YL++HRP W A  AVGKT+VSSS+IDRV
Sbjct: 300 ATGNDADADRHGIVTPDGGLMNPNHYLAAAISYLFSHRPGWGADTAVGKTLVSSSMIDRV 359

Query: 362 VAGIGRQLVEVPVGFKWFVDGLIGATLGFGGEESAGASFLRRDGSVWTTDKDGIIMALLA 421
           V+G+GR+L+EVPVGFK+FV GL+  ++GFGGEESAGA+FLR DG VWTTDKDGI +ALLA
Sbjct: 360 VSGLGRRLLEVPVGFKYFVPGLLDGSVGFGGEESAGAAFLRHDGGVWTTDKDGIQLALLA 419

Query: 422 AEILAVTGATPSQRYHALAGEYGGPCYARIDAPADREQKARLARLSADQVSATELAGEPI 481
           AEI AVTG + SQ Y  L  +YG P YAR+DAPA RE+KARL++LS   VSA  LAGE I
Sbjct: 420 AEIQAVTGKSASQLYAGLTDQYGAPAYARVDAPASREEKARLSKLSPSDVSAKTLAGEAI 479

Query: 482 TAKLTTAPGNGAALGGLKVTTANAWFAARPSGTEDVYKIYAESFRGPQHLVEVQQTAREV 541
           T  LT APGNG A+GGLKV T NAWFAARPSGTEDVYK+YAESF G  HL +VQ  AREV
Sbjct: 480 TDILTAAPGNGEAIGGLKVCTQNAWFAARPSGTEDVYKVYAESFLGADHLKQVQAEAREV 539

Query: 542 V 542
           V
Sbjct: 540 V 540


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: 1066
Number of extensions: 36
Number of successful extensions: 4
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: 546
Length adjustment: 36
Effective length of query: 511
Effective length of database: 510
Effective search space:   260610
Effective search space used:   260610
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 CCNA_00083 CCNA_00083 (phosphoglucomutase/phosphomannomutase)
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.25953.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-273  894.6   0.9   1.1e-273  894.5   0.9    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_00083  CCNA_00083 phosphoglucomutase/ph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_00083  CCNA_00083 phosphoglucomutase/phosphomannomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  894.5   0.9  1.1e-273  1.1e-273       3     546 .]       2     545 ..       1     545 [. 0.99

  Alignments for each domain:
  == domain 1  score: 894.5 bits;  conditional E-value: 1.1e-273
                             TIGR01132   3 inpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevraaq 75 
                                           +++raG +a +edl+d+ +l+ +y+ +kpd  n+aqkv fGtsGhrGs+l g+fneahila++qa+ve+raaq
  lcl|FitnessBrowser__Caulo:CCNA_00083   2 MHDRAGLRALPEDLVDLDALIGAYFEIKPDVSNPAQKVVFGTSGHRGSSLDGAFNEAHILAVTQAIVEYRAAQ 74 
                                           89*********************************************************************** PP

                             TIGR01132  76 GitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkealadGivitpsh 148
                                           G+tGpl++G+dth+lsepa+ svlevlaan+ve++v++++++tptpavshailt+n+ + + +adG+++tpsh
  lcl|FitnessBrowser__Caulo:CCNA_00083  75 GVTGPLFVGRDTHGLSEPAWRSVLEVLAANGVEALVDSRDGFTPTPAVSHAILTHNR-QGGRQADGLLLTPSH 146
                                           *********************************************************.99************* PP

                             TIGR01132 149 nppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladvvd 221
                                           npp+dGGikynpp+GGpa +++t ai+ ranell+++l+gvkr+++e+a k   v + d++ +yvddl+ v+d
  lcl|FitnessBrowser__Caulo:CCNA_00083 147 NPPRDGGIKYNPPSGGPAGSDATSAIAARANELLAQGLAGVKRVPFETARK--AVGDYDFLGRYVDDLPAVID 217
                                           *************************************************99..899***************** PP

                             TIGR01132 222 laairkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagllkl 294
                                           +aair a++r+G+dplGGa+v yw  iae++ ldlt+vn+avd+ + fm ld+dGkirmdcss  ama+l+ +
  lcl|FitnessBrowser__Caulo:CCNA_00083 218 IAAIRAAKVRIGADPLGGAAVAYWGAIAERHALDLTVVNDAVDPRWAFMPLDTDGKIRMDCSSSSAMANLIGI 290
                                           ********************************************************************99985 PP

                             TIGR01132 295 k...dkydlafgndadadrhGivtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadl 364
                                                 yd+a+gndadadrhGivtpd Gl+npnhyla ai+yl++hr++w+a++avGktlvss++idrvv+ l
  lcl|FitnessBrowser__Caulo:CCNA_00083 291 MkggAAYDVATGNDADADRHGIVTPDGGLMNPNHYLAAAISYLFSHRPGWGADTAVGKTLVSSSMIDRVVSGL 363
                                           412268******************************************************************* PP

                             TIGR01132 365 grklvevpvGfkwfvdGlldgslGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqryde 437
                                           gr+l+evpvGfk+fv Glldgs+GfGGeesaGa+flr+dG vw+tdkdGi lallaaei avtGk+ +q y  
  lcl|FitnessBrowser__Caulo:CCNA_00083 364 GRRLLEVPVGFKYFVPGLLDGSVGFGGEESAGAAFLRHDGGVWTTDKDGIQLALLAAEIQAVTGKSASQLYAG 436
                                           ************************************************************************* PP

                             TIGR01132 438 laakyGdpiyaridaaatsaqkarlkklspdevsattlaGdaitakltkapGngaaiGGlkvttdegwfaarp 510
                                           l+ +yG+p+yar+da+a++++karl+klsp +vsa+tlaG+ait  lt+apGng aiGGlkv t+++wfaarp
  lcl|FitnessBrowser__Caulo:CCNA_00083 437 LTDQYGAPAYARVDAPASREEKARLSKLSPSDVSAKTLAGEAITDILTAAPGNGEAIGGLKVCTQNAWFAARP 509
                                           ************************************************************************* PP

                             TIGR01132 511 sGtedvykiyaesfkgeehlkeiekeaeeivdevlk 546
                                           sGtedvyk+yaesf g++hlk+++ ea+e+v  +lk
  lcl|FitnessBrowser__Caulo:CCNA_00083 510 SGTEDVYKVYAESFLGADHLKQVQAEAREVVAGALK 545
                                           *******************************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (546 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 7.20
//
[ok]

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:

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