Alignments for a candidate for manA in Psychromonas ossibalaenae JAMM 0738

GapMind for catabolism of small carbon sources

Alignments for a candidate for manA in Psychromonas ossibalaenae JAMM 0738

Align mannose-6-phosphate isomerase (EC 5.3.1.8) (characterized)
to candidate WP_019617264.1 G327_RS0123570 mannose-6-phosphate isomerase, class I

Query= ecocyc::MANNPISOM-MONOMER
         (391 letters)



>NCBI__GCF_000381745.1:WP_019617264.1
          Length = 396

 Score =  311 bits (798), Expect = 2e-89
 Identities = 177/391 (45%), Positives = 231/391 (59%), Gaps = 6/391 (1%)

Query: 3   KLINSVQNYAWGSKTALTELYGMENPSSQPMAELWMGAHPKSSSRVQNAAGDIVSLRDVI 62
           K+ N++QNY WGSKTA+  L+  +N S+Q  AELWMGAHP   S +    G++  L D I
Sbjct: 8   KMTNTIQNYDWGSKTAMQNLFSFQNNSAQRQAELWMGAHPNGCSLLL-IEGELTKLSDFI 66

Query: 63  ESDKSTLLGEAVAKRFGELPFLFKVLCAAQPLSIQVHPNKHNSEIGFAKENAAGIPMDAA 122
             D   +LGE  A  FG+LP+LFKVL A + LS+QVHPNK  ++ GF KEN  GI  +A 
Sbjct: 67  AQDPQLILGEKTADEFGQLPYLFKVLAAEKALSVQVHPNKQQAQEGFDKENQLGISCNAF 126

Query: 123 ERNYKDPNHKPELVFALTPFLAMNAFREFSEIVSLLQ--PVAGAHPAIAHFLQQPDAERL 180
           +RNYKD NHKPE+VFALT + AMN FR  +EI+   Q   +      +  F      + L
Sbjct: 127 DRNYKDSNHKPEVVFALTEYQAMNGFRSPAEILKHFQLLNILELEQLVEAFSDNLTEDGL 186

Query: 181 SELFASLLNMQGEEKSRALAILKSALDSQQGEP-WQTIRLISEFYPEDSGLFSPLLLNVV 239
              F  +L ++GE K  AL  L     +    P +  I  +   +P D GLFSPL+LNV+
Sbjct: 187 QTFFQVMLLLEGEHKMNALQALSIYAKNNLYNPLFHLIADLETQHPGDIGLFSPLMLNVL 246

Query: 240 KLNPGEAMFLFAETPHAYLQGVALEVMANSDNVLRAGLTPKYIDIPELVANVKFEAKPAN 299
            L  GEAMFL A TPHAY++G  LE+MANSDNVLRAGLTPKYID+PELVAN  F +    
Sbjct: 247 TLQAGEAMFLDACTPHAYIKGTGLEIMANSDNVLRAGLTPKYIDVPELVANTIFTSVMTE 306

Query: 300 QLLTQPVKQGAELDFPIPVDDFAFSLHDLSDKETTISQQSAAILFCVEGDATL-WKGSQQ 358
            LL +   +    ++ +PV DF FS+ D +  E  +   SA I+F V+    L  +    
Sbjct: 307 NLLLKEKSEEGWQNYIVPVPDFKFSVAD-NVSELNVKVNSAEIVFAVDSQVRLNHRNGST 365

Query: 359 LQLKPGESAFIAANESPVTVKGHGRLARVYN 389
           + +K GES FI A      V   G+LAR YN
Sbjct: 366 ITIKKGESVFIPAYVDHYQVTTSGQLARAYN 396


Lambda     K      H
   0.316    0.132    0.379 

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: 419
Number of extensions: 21
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: 391
Length of database: 396
Length adjustment: 31
Effective length of query: 360
Effective length of database: 365
Effective search space:   131400
Effective search space used:   131400
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: 50 (23.9 bits)

Align candidate WP_019617264.1 G327_RS0123570 (mannose-6-phosphate isomerase, class I)
to HMM TIGR00218 (manA: mannose-6-phosphate isomerase, class I (EC 5.3.1.8))

# 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/TIGR00218.hmm
# target sequence database:        /tmp/gapView.794000.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00218  [M=359]
Accession:   TIGR00218
Description: manA: mannose-6-phosphate isomerase, class I
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    3.6e-90  288.6   0.4    4.6e-90  288.3   0.4    1.0  1  NCBI__GCF_000381745.1:WP_019617264.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000381745.1:WP_019617264.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  288.3   0.4   4.6e-90   4.6e-90       4     352 ..       6     388 ..       4     394 .. 0.89

  Alignments for each domain:
  == domain 1  score: 288.3 bits;  conditional E-value: 4.6e-90
                             TIGR00218   4 lfrvqknlkerdWGkgtaladllgysipskq.taElWagaHkkgsSkvqn.gkkvsLrdliekhksellGkae 74 
                                           + ++ + ++++dWG++ta+++l+ ++++s q  aElW+gaH++g S  +  g+   L+d+i ++++ +lG++ 
  NCBI__GCF_000381745.1:WP_019617264.1   6 FYKMTNTIQNYDWGSKTAMQNLFSFQNNSAQrQAELWMGAHPNGCSLLLIeGELTKLSDFIAQDPQLILGEKT 78 
                                           5689999*********************9988***************99878********************* PP

                             TIGR00218  75 adrf.elPlLvkvLsaekplsiqvHPdkalakigyake..........krnYkDknhkpelvialtdfealkg 136
                                           ad f +lP L+kvL aek ls+qvHP+k+ a+ g++ke          +rnYkD nhkpe+v+alt+++a++g
  NCBI__GCF_000381745.1:WP_019617264.1  79 ADEFgQLPYLFKVLAAEKALSVQVHPNKQQAQEGFDKEnqlgiscnafDRNYKDSNHKPEVVFALTEYQAMNG 151
                                           ************************************************************************* PP

                             TIGR00218 137 fkp.........Lkriaelh...............eeaerlgkteawviiasdekikeaaeilkealkns.ke 184
                                           f+          L     l+                e+  l+  +  ++   +e++ +a + l    kn+  +
  NCBI__GCF_000381745.1:WP_019617264.1 152 FRSpaeilkhfqL-----LNileleqlveafsdnlTEDG-LQTFFQVMLLLEGEHKMNALQALSIYAKNNlYN 218
                                           **98888555552.....334444466666665434444.9****9999999999999999998888888455 PP

                             TIGR00218 185 elkekiqrl..iypedvglfkgllLnrvklkpgeaiyvrsgtvHAykggdvlEvmanSdnvvragltdkyldv 255
                                            l ++i  l  ++p d+glf++l Ln++ l++gea+++ + t+HAy++g  lE+manSdnv+raglt+ky+dv
  NCBI__GCF_000381745.1:WP_019617264.1 219 PLFHLIADLetQHPGDIGLFSPLMLNVLTLQAGEAMFLDACTPHAYIKGTGLEIMANSDNVLRAGLTPKYIDV 291
                                           55566666688************************************************************** PP

                             TIGR00218 256 kklvevltveekpeeklkeqkqkegaevlflvpieefavlktdlsekaelksqdsalillvleGdglil.sge 327
                                           ++lv++  ++++  e+l  +++ e+    + vp+ +f+++  d   ++   +++sa i+++++ + ++  +++
  NCBI__GCF_000381745.1:WP_019617264.1 292 PELVANTIFTSVMTENLLLKEKSEEGWQNYIVPVPDFKFSVADNVSEL-NVKVNSAEIVFAVDSQVRLNhRNG 363
                                           *************999999998888899************99877777.46799**********999962678 PP

                             TIGR00218 328 kklklkkGesfliaakleevtiege 352
                                            ++ +kkGes++i+a ++  ++   
  NCBI__GCF_000381745.1:WP_019617264.1 364 STITIKKGESVFIPAYVDHYQVTTS 388
                                           99*************9999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (359 nodes)
Target sequences:                          1  (396 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 18.33
//
[ok]

This GapMind analysis is from Sep 24 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