Alignments for a candidate for prpB in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpB in Herbaspirillum seropedicae SmR1

Align 2-methylcitrate lyase (EC 4.1.3.30) (characterized)
to candidate HSERO_RS15660 HSERO_RS15660 2-methylisocitrate lyase

Query= metacyc::MONOMER-13636
         (302 letters)



>FitnessBrowser__HerbieS:HSERO_RS15660
          Length = 296

 Score =  495 bits (1274), Expect = e-145
 Identities = 249/292 (85%), Positives = 270/292 (92%)

Query: 11  SAGARFRQALADEHPLQVVGTINANHALLAKRAGYRAIYLSGGGVAAGSLGLPDLGISNL 70
           SAGA FR+A+ +E PLQV+G INANHALLAKRAG+RAIYLSGGGVAAGSLGLPDLGISNL
Sbjct: 5   SAGAAFRKAVQEESPLQVIGAINANHALLAKRAGFRAIYLSGGGVAAGSLGLPDLGISNL 64

Query: 71  DDVLTDIRRITDVCDTPLLVDVDTGFGASAFNVARTTKSLIKFGAAAMHIEDQVGAKRCG 130
           DDVLTD+RRITDVCD PLLVDVDTGFGASAFNVART KS+IKFGAAAMHIEDQVGAKRCG
Sbjct: 65  DDVLTDVRRITDVCDLPLLVDVDTGFGASAFNVARTVKSMIKFGAAAMHIEDQVGAKRCG 124

Query: 131 HRPNKEIVTQGEMVDRIRAAVDARTDENFVIMARTDALAVEGLDKAIERAVACAEAGADA 190
           HRPNKEIV++ EMVDRI+AAVDARTDENFVIMARTDALAVEGLD AIERAVAC EAGAD 
Sbjct: 125 HRPNKEIVSKQEMVDRIKAAVDARTDENFVIMARTDALAVEGLDAAIERAVACVEAGADM 184

Query: 191 IFPEAMTDLAMYRKFVDAVKVPVLANITEFGATPLFTTEELGGAGVSMVLYPLSAFRAMN 250
           IFPEA+TDLAMY++F +AVKVP+LANITEFG+TPLFT +EL GA V +VLYPLSAFRAMN
Sbjct: 185 IFPEAITDLAMYKQFANAVKVPILANITEFGSTPLFTVDELKGADVGLVLYPLSAFRAMN 244

Query: 251 KAAENVYAAIRRDGTQKNVVDTMQTRAELYESIGYHDFEQKLDALFAQGKGK 302
           KAAENVY AIRRDGTQKNVVDTMQTR ELY+ I YH +EQ+LDALFAQ K K
Sbjct: 245 KAAENVYQAIRRDGTQKNVVDTMQTRMELYDRIDYHSYEQRLDALFAQQKNK 296


Lambda     K      H
   0.320    0.134    0.376 

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: 364
Number of extensions: 6
Number of successful extensions: 1
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: 302
Length of database: 296
Length adjustment: 27
Effective length of query: 275
Effective length of database: 269
Effective search space:    73975
Effective search space used:    73975
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: 48 (23.1 bits)

Align candidate HSERO_RS15660 HSERO_RS15660 (2-methylisocitrate lyase)
to HMM TIGR02317 (prpB: methylisocitrate lyase (EC 4.1.3.30))

# 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/TIGR02317.hmm
# target sequence database:        /tmp/gapView.20891.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02317  [M=285]
Accession:   TIGR02317
Description: prpB: methylisocitrate lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   5.6e-136  438.3   3.5   6.5e-136  438.1   3.5    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS15660  HSERO_RS15660 2-methylisocitrate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS15660  HSERO_RS15660 2-methylisocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  438.1   3.5  6.5e-136  6.5e-136       2     284 ..       7     291 ..       6     292 .. 0.99

  Alignments for each domain:
  == domain 1  score: 438.1 bits;  conditional E-value: 6.5e-136
                                  TIGR02317   2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevaeearri 68 
                                                g+a+r+++++e++lq++Gaina++alla++aGf+a+YlsG+++aa slglPDlg+++l++v++++rri
  lcl|FitnessBrowser__HerbieS:HSERO_RS15660   7 GAAFRKAVQEESPLQVIGAINANHALLAKRAGFRAIYLSGGGVAAgSLGLPDLGISNLDDVLTDVRRI 74 
                                                679****************************************999********************** PP

                                  TIGR02317  69 trvtklpllvDaDtGfGe.alnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkik 135
                                                t+v++lpllvD+DtGfG  a+nvartvk++++ g+aa+hieDqv +k+CGh+++ke+vsk+emv++ik
  lcl|FitnessBrowser__HerbieS:HSERO_RS15660  75 TDVCDLPLLVDVDTGFGAsAFNVARTVKSMIKFGAAAMHIEDQVGAKRCGHRPNKEIVSKQEMVDRIK 142
                                                *****************879************************************************ PP

                                  TIGR02317 136 aavkakkdedfvliaRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllan 203
                                                aav+a++de+fv++aRtDa aveGldaaieRa a veaGad+if+ea+++++++++fa+avkvp+lan
  lcl|FitnessBrowser__HerbieS:HSERO_RS15660 143 AAVDARTDENFVIMARTDALAVEGLDAAIERAVACVEAGADMIFPEAITDLAMYKQFANAVKVPILAN 210
                                                ******************************************************************** PP

                                  TIGR02317 204 mtefGktplltadeleelgykiviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellg 271
                                                +tefG tpl+t+del+ + + +v+yP++a+Ra++kaae+vy+ ++++Gtqk+++d++qtR elY+ ++
  lcl|FitnessBrowser__HerbieS:HSERO_RS15660 211 ITEFGSTPLFTVDELKGADVGLVLYPLSAFRAMNKAAENVYQAIRRDGTQKNVVDTMQTRMELYDRID 278
                                                ******************************************************************** PP

                                  TIGR02317 272 yedyekkdkelfk 284
                                                y++ye++++ lf+
  lcl|FitnessBrowser__HerbieS:HSERO_RS15660 279 YHSYEQRLDALFA 291
                                                ********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (296 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: 6.98
//
[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