Alignments for a candidate for pgmA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Herbaspirillum seropedicae SmR1

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate HSERO_RS13360 HSERO_RS13360 phosphoglucomutase

Query= BRENDA::A0A0H3NJ17
         (546 letters)



>FitnessBrowser__HerbieS:HSERO_RS13360
          Length = 549

 Score =  616 bits (1589), Expect = 0.0
 Identities = 314/545 (57%), Positives = 395/545 (72%), Gaps = 2/545 (0%)

Query: 2   AIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAGRHSFNEPHI 61
           +++  AGQ A  S L+++  L + YY L+P+   A H V FGTSGHRG+A  HSFNE H+
Sbjct: 3   SVNPLAGQRAAPSALVDLPVLVSNYYSLRPDVAEASHRVAFGTSGHRGNANAHSFNEWHV 62

Query: 62  LAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPTP 121
           LAI QAI + R + G  GP ++G DTHALSEPA+ S LEVLAAN V  ++ E + + PTP
Sbjct: 63  LAITQAICDYRKEQGFKGPLFLGIDTHALSEPAWHSALEVLAANEVVTMLAEGSPYAPTP 122

Query: 122 AVSNAILVHNK-KGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANAL 180
           AVS+AIL HN+     LADGIV+TPSHNPP++GG KYN PNGGP+D+NVT  +E RANA 
Sbjct: 123 AVSHAILTHNRVHRDALADGIVVTPSHNPPDNGGFKYNMPNGGPSDSNVTGWIEQRANAY 182

Query: 181 LAGGLQGVKRISLDAAMASGHVKAVDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLGGSG 240
           L   LQGV+R+S + A+ +   +  D +  +V  L +I+D+AAI  A + +GVDPLGG+G
Sbjct: 183 LEQQLQGVRRVSFEKALKADTTRRYDYLDNYVSDLPNIIDLAAISGANVKIGVDPLGGAG 242

Query: 241 IEYWKRIAEHYKLNLTLVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDLA 300
           + YW  IA+ YKLNL +VN +VD TFRF+ LD D  IRMD SS  AM+ L+AL+D+FD+A
Sbjct: 243 LHYWSAIADRYKLNLEVVNTEVDATFRFVPLDWDAQIRMDPSSPHAMSELIALKDRFDVA 302

Query: 301 FANDPDYDRHGIVTPA-GLMNPNHYLAVAINYLFQHRPLWGKDVAVGKTLVSSAMIDRVV 359
            A D D+DRHGIV  + GLM  N YL+VA+ YLF+HRP W  D A+GKTLVSS MI+RV 
Sbjct: 303 MACDTDHDRHGIVAKSRGLMPANDYLSVAVYYLFRHRPAWRADAAIGKTLVSSQMINRVA 362

Query: 360 NDLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAA 419
             L RKL+E+PVGFKWFVDGL+DGS  FG EESAGASF+RFDG PWSTDKDGI   LLAA
Sbjct: 363 KHLERKLLEMPVGFKWFVDGLYDGSLAFGCEESAGASFVRFDGQPWSTDKDGITAALLAA 422

Query: 420 EITAVTGKNPQEHYNELAARFGAPSYNRLQASATSAQKAALSKLSPEMVSASTLAGDPIT 479
           E+TA TG +P + Y +L  + GAP   R +A+AT  QKA LSKLSP+ VS++ LAG+PI 
Sbjct: 423 EMTARTGNDPGQIYEDLTHQLGAPLNGRKEAAATPEQKARLSKLSPQDVSSTELAGEPIR 482

Query: 480 ARLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEIV 539
             LT AP NG   GGLK++TDNGWFAARPSGTE  YKIY ESF  + H  +I  EA +IV
Sbjct: 483 EVLTTAPANGKPFGGLKIVTDNGWFAARPSGTESIYKIYGESFRDQAHLDKIFAEAQDIV 542

Query: 540 SEVLK 544
           +  L+
Sbjct: 543 TRALQ 547


Lambda     K      H
   0.316    0.134    0.395 

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: 895
Number of extensions: 38
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: 546
Length of database: 549
Length adjustment: 36
Effective length of query: 510
Effective length of database: 513
Effective search space:   261630
Effective search space used:   261630
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 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate HSERO_RS13360 HSERO_RS13360 (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.18158.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   4.7e-259  846.2   0.0   5.5e-259  846.0   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS13360  HSERO_RS13360 phosphoglucomutase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS13360  HSERO_RS13360 phosphoglucomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  846.0   0.0  5.5e-259  5.5e-259       2     545 ..       3     546 ..       2     547 .. 1.00

  Alignments for each domain:
  == domain 1  score: 846.0 bits;  conditional E-value: 5.5e-259
                                  TIGR01132   2 ainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavv 69 
                                                ++np+aGq+a ++ l+d++ lv++yy+l+pd  +a+++v+fGtsGhrG a+ ++fne h+lai+qa+ 
  lcl|FitnessBrowser__HerbieS:HSERO_RS13360   3 SVNPLAGQRAAPSALVDLPVLVSNYYSLRPDVAEASHRVAFGTSGHRGNANAHSFNEWHVLAITQAIC 70 
                                                689***************************************************************** PP

                                  TIGR01132  70 evraaqGitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkea 137
                                                ++r++qG  Gpl++G dthalsepa+ s+levlaan+v++++ e + y+ptpavshailt+n+ +++a
  lcl|FitnessBrowser__HerbieS:HSERO_RS13360  71 DYRKEQGFKGPLFLGIDTHALSEPAWHSALEVLAANEVVTMLAEGSPYAPTPAVSHAILTHNRVHRDA 138
                                                ******************************************************************** PP

                                  TIGR01132 138 ladGivitpshnppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvke 205
                                                ladGiv+tpshnpp++GG+kyn pnGGp++++vt +ie+ran++l+++l+gv+r+++ekalk++t+++
  lcl|FitnessBrowser__HerbieS:HSERO_RS13360 139 LADGIVVTPSHNPPDNGGFKYNMPNGGPSDSNVTGWIEQRANAYLEQQLQGVRRVSFEKALKADTTRR 206
                                                ******************************************************************** PP

                                  TIGR01132 206 kdlvkpyvddladvvdlaairkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtld 273
                                                 d++++yv dl++++dlaai  a++++GvdplGGag++yw  ia++y+l+l +vn +vdatfrf+ ld
  lcl|FitnessBrowser__HerbieS:HSERO_RS13360 207 YDYLDNYVSDLPNIIDLAAISGANVKIGVDPLGGAGLHYWSAIADRYKLNLEVVNTEVDATFRFVPLD 274
                                                ******************************************************************** PP

                                  TIGR01132 274 kdGkirmdcsspyamagllklkdkydlafgndadadrhGivtpdkGllnpnhylavaieylykhrqqw 341
                                                +d +irmd ssp+am+ l++lkd++d+a++ d+d drhGiv+ ++Gl+  n yl+va+ yl++hr+ w
  lcl|FitnessBrowser__HerbieS:HSERO_RS13360 275 WDAQIRMDPSSPHAMSELIALKDRFDVAMACDTDHDRHGIVAKSRGLMPANDYLSVAVYYLFRHRPAW 342
                                                ******************************************************************** PP

                                  TIGR01132 342 aaevavGktlvssalidrvvadlgrklvevpvGfkwfvdGlldgslGfGGeesaGasflrkdGtvwst 409
                                                 a+ a+Gktlvss +i+rv+ +l+rkl+e+pvGfkwfvdGl+dgsl fG eesaGasf+r+dG +wst
  lcl|FitnessBrowser__HerbieS:HSERO_RS13360 343 RADAAIGKTLVSSQMINRVAKHLERKLLEMPVGFKWFVDGLYDGSLAFGCEESAGASFVRFDGQPWST 410
                                                ******************************************************************** PP

                                  TIGR01132 410 dkdGiilallaaeitavtGknpqqrydelaakyGdpiyaridaaatsaqkarlkklspdevsattlaG 477
                                                dkdGi  allaae+ta tG++p+q y++l+ ++G+p+  r +aaat++qkarl+klsp++vs+t+laG
  lcl|FitnessBrowser__HerbieS:HSERO_RS13360 411 DKDGITAALLAAEMTARTGNDPGQIYEDLTHQLGAPLNGRKEAAATPEQKARLSKLSPQDVSSTELAG 478
                                                ******************************************************************** PP

                                  TIGR01132 478 daitakltkapGngaaiGGlkvttdegwfaarpsGtedvykiyaesfkgeehlkeiekeaeeivdevl 545
                                                ++i   lt+ap ng   GGlk++td+gwfaarpsGte +ykiy esf++++hl +i+ ea++iv+++l
  lcl|FitnessBrowser__HerbieS:HSERO_RS13360 479 EPIREVLTTAPANGKPFGGLKIVTDNGWFAARPSGTESIYKIYGESFRDQAHLDKIFAEAQDIVTRAL 546
                                                *****************************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (549 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: 00:00:00.03
# Mc/sec: 7.81
//
[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