Alignments for a candidate for mmsA in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Pseudomonas fluorescens FW300-N1B4

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate Pf1N1B4_4277 Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27)

Query= BRENDA::G5CZI2
         (498 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4277
          Length = 500

 Score =  618 bits (1594), Expect = 0.0
 Identities = 301/496 (60%), Positives = 381/496 (76%), Gaps = 3/496 (0%)

Query: 4   IGHLINGQLVT-ENTRSQNVFNPATGEIGKQLDLASTKTVEQAISAAQHAFPTWRNTPPL 62
           IGH I+GQ+    + R  NVFNPATG I  ++ LAS KTV+ A+++A  AFP W     L
Sbjct: 7   IGHYIDGQVQDCGSERFSNVFNPATGSIQARVGLASQKTVDDAVASALKAFPAWSEQSSL 66

Query: 63  KRARVMFRFKELLEQHADEICRLIGEEHGKIAHDAMGELQRGIENVEYACGAPELLKGEH 122
           +R+RVMF+FKELL++H +E+  +I  EHGK+  DA GE+ RGIE VEYACGAP LLK + 
Sbjct: 67  RRSRVMFKFKELLDRHHNELAEIISREHGKVFSDAKGEVTRGIEIVEYACGAPNLLKTDF 126

Query: 123 SRNVGPGIDSWSEFQPMGVVAGITPFNFPVMVPLWMFPMAIVCGNCFVLKPSERDPSSTL 182
           S N+G GID+W+  QP+GV AG+TPFNFPVMVPLWM P+A+V GNCF+LKPSERDPS++L
Sbjct: 127 SDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVTGNCFILKPSERDPSASL 186

Query: 183 YIAQLLQEAGLPDGVMNVVNGDKEAVDALLHDDRVKAVSFVGSTPIAEYIYRTASANGKR 242
            +A+LL EAGLPDGV NVV GDK AVDALL    ++A+SFVGSTPIAEYI++ A++ GKR
Sbjct: 187 LMAKLLTEAGLPDGVFNVVQGDKAAVDALLQHPDIEAISFVGSTPIAEYIHQQATSRGKR 246

Query: 243 CQALGGAKNHAIVMPDADMDNAVNQLLGAAFGSSGERCMALSVAVAVGDAAGDALVSKMT 302
            QALGGAKNH IVMPDAD+D A + L+GAA+GS+GERCMA+S+AV VGD  GD L++K+ 
Sbjct: 247 VQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVTVGD-VGDQLIAKLL 305

Query: 303 QAMQKLKVGPSTDSGNDFGPVITRQHQEKVIGYINSAEQQGATIVVDGRQPKVPNHENGF 362
             + +LKVG      +D GP++T +H+ KV G+I     QGA ++VDGR  KVP  ENGF
Sbjct: 306 PRIDQLKVGNGMQGDSDMGPLVTAEHKAKVEGFIGEGVAQGAQLIVDGRNFKVPGAENGF 365

Query: 363 FVGGTLIDHVTPEMTSYQEEIFGPVLQVVRVATMQDAMDLIDAHEYGNGTCIFTRDGEAA 422
           FVG TL D+VT EM+ YQ+EIFGPVL +VRV     A+ LI+AHE+GNG   FT DG  A
Sbjct: 366 FVGATLFDNVTTEMSIYQQEIFGPVLGIVRVPDFASAVALINAHEFGNGVSCFTSDGGIA 425

Query: 423 RYFSDNIQVGMVGINIPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTKRKTVTQRWP 482
           R F+ NI+VGMVGIN+P+PVP+A+HSFGGWKRSLFGD HAYG + +RFY++ K+V QRWP
Sbjct: 426 RSFARNIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGIRFYSRYKSVMQRWP 485

Query: 483 SAGVREGAEFSMPTMK 498
            + + +G EFSMPT K
Sbjct: 486 DS-IAKGPEFSMPTAK 500


Lambda     K      H
   0.319    0.135    0.405 

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: 752
Number of extensions: 27
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: 498
Length of database: 500
Length adjustment: 34
Effective length of query: 464
Effective length of database: 466
Effective search space:   216224
Effective search space used:   216224
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate Pf1N1B4_4277 (Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27))
to HMM TIGR01722 (mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27))

# 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/TIGR01722.hmm
# target sequence database:        /tmp/gapView.480.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01722  [M=477]
Accession:   TIGR01722
Description: MMSDH: methylmalonate-semialdehyde dehydrogenase (acylating)
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.1e-211  689.5   0.2   1.3e-211  689.3   0.2    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4277  Methylmalonate-semialdehyde dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4277  Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  689.3   0.2  1.3e-211  1.3e-211       2     477 .]       8     484 ..       7     484 .. 1.00

  Alignments for each domain:
  == domain 1  score: 689.3 bits;  conditional E-value: 1.3e-211
                                      TIGR01722   2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarv 65 
                                                     h+idG++ +  s+++ +v npat+++ a+v  as++ vd avasa ++f+aw+e s ++r+rv
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4277   8 GHYIDGQVQDCGSERFSNVFNPATGSIQARVGLASQKTVDDAVASALKAFPAWSEQSSLRRSRV 71 
                                                    59************************************************************** PP

                                      TIGR01722  66 llryqallkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvd 129
                                                    ++++++ll+ h++e+a++is e+Gk+++dakG+v rG+e+ve+ac+ + ll+ + ++++   +d
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4277  72 MFKFKELLDRHHNELAEIISREHGKVFSDAKGEVTRGIEIVEYACGAPNLLKTDFSDNIGGGID 135
                                                    **************************************************************** PP

                                      TIGR01722 130 vysirqplGvvaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapd 193
                                                     + +rqplGv+aG+tpfnfp m+plwm pla++ Gn+f+lkpse++psa++ +a+ll+eaG+pd
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4277 136 NWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVTGNCFILKPSERDPSASLLMAKLLTEAGLPD 199
                                                    **************************************************************** PP

                                      TIGR01722 194 GvlnvvhGdkeavdrllehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpda 257
                                                    Gv+nvv Gdk avd ll+hpd+ a+sfvGs++++eyi+++++++gkrvqal+Gaknhm+v+pda
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4277 200 GVFNVVQGDKAAVDALLQHPDIEAISFVGSTPIAEYIHQQATSRGKRVQALGGAKNHMIVMPDA 263
                                                    **************************************************************** PP

                                      TIGR01722 258 dkeaaldalvgaavGaaGqrcmaisaavlvGaa.kelveeireraekvrvgagddpgaelGpli 320
                                                    d+++a+dal+gaa+G+aG+rcmais+av vG++ ++l+ ++  r+++++vg g +  +++Gpl+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4277 264 DLDQAADALIGAAYGSAGERCMAISIAVTVGDVgDQLIAKLLPRIDQLKVGNGMQGDSDMGPLV 327
                                                    *********************************9****************************** PP

                                      TIGR01722 321 tkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvl 384
                                                    t ++k++v+ +i++g+++Ga++++dGr++kv G e+G fvG tl+++v ++m+iy++eifGpvl
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4277 328 TAEHKAKVEGFIGEGVAQGAQLIVDGRNFKVPGAENGFFVGATLFDNVTTEMSIYQQEIFGPVL 391
                                                    **************************************************************** PP

                                      TIGR01722 385 vvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGw 448
                                                     ++++  +  a++lin+  +GnG + ftsdG+ ar f  +i+vG+vG+nvpipvp++++sf+Gw
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4277 392 GIVRVPDFASAVALINAHEFGNGVSCFTSDGGIARSFARNIKVGMVGINVPIPVPMAWHSFGGW 455
                                                    **************************************************************** PP

                                      TIGR01722 449 kdslfGdlhiyGkqGvrfytrlktvtarw 477
                                                    k slfGd+h+yG++G+rfy+r k v  rw
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4277 456 KRSLFGDHHAYGEEGIRFYSRYKSVMQRW 484
                                                    ****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (500 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: 00:00:00.03
# Mc/sec: 7.40
//
[ok]

This GapMind analysis is from Sep 17 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