Alignments for a candidate for manA in Methylohalobius crimeensis 10Ki

GapMind for catabolism of small carbon sources

Alignments for a candidate for manA in Methylohalobius crimeensis 10Ki

Align mannose-6-phosphate isomerase (EC 5.3.1.8) (characterized)
to candidate WP_022947775.1 H035_RS18120 mannose-6-phosphate isomerase, class I

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



>NCBI__GCF_000421465.1:WP_022947775.1
          Length = 416

 Score =  236 bits (603), Expect = 7e-67
 Identities = 151/375 (40%), Positives = 205/375 (54%), Gaps = 16/375 (4%)

Query: 4   LINSVQNYAWGSKTALTELYGMENPSSQPMAELWMGAHPKSSSRVQNAAGDIVSLRDVIE 63
           L   VQ YAWG    +  L G  NP   P AELW+GAHP   ++        VSL D++ 
Sbjct: 26  LFCGVQQYAWGDFDFIPRLLGKTNPDRDPFAELWIGAHPDLPAQAV-IGRTRVSLSDLLP 84

Query: 64  SDKSTLLGEAVAKRF-GELPFLFKVLCAAQPLSIQVHPNKHNSEIGFAKENAAGIPMDAA 122
                LLG     R+ G+LPFL K+L A +PLSIQVHP+KH +E GFA+E+   IP+D+ 
Sbjct: 85  EAVECLLGADAKIRYQGQLPFLMKILAAGRPLSIQVHPDKHQAEAGFAREHRLKIPLDSP 144

Query: 123 ERNYKDPNHKPELVFALTPFLAMNAFREFSEIVSLLQPVAGAHPAIAHFLQQPDAERLSE 182
            RNY+D NHKPEL+ ALT F A+  FR  SEI   L  +    P      ++   E L +
Sbjct: 145 RRNYRDCNHKPELLCALTDFYALKGFRPESEIADQLASI----PEWRGLAERFRDEGLKK 200

Query: 183 LFASLLNMQGEEKSRALAILKSAL------DSQQGEPW--QTIRLISEFYPEDSGLFSPL 234
            +  L+ +        LA + + L         + E W  +   L S+    D GLFS  
Sbjct: 201 FYYHLMTLPQSVVDEMLAPVVARLRWEGPFPKDRREYWLLRADELYSQGAHHDRGLFSLY 260

Query: 235 LLNVVKLNPGEAMFLFAETPHAYLQGVALEVMANSDNVLRAGLTPKYIDIPELVANVKFE 294
           LLN + L PGEA+F  A   H+YL+GV +EVMANS+NVLR GLTPK++D+P L+  VKFE
Sbjct: 261 LLNFLCLRPGEAIFQHAGELHSYLEGVGVEVMANSNNVLRGGLTPKHVDVPALLEIVKFE 320

Query: 295 AKPANQLLTQPVKQGAELDFPIPVDDFAFSLHDLSDKETTISQQSAAILFCVEGDATLWK 354
            K A  L ++  + GA   +P PVD+F  S  DLS   T  S+    +   +EG   +  
Sbjct: 321 GKKAEILSSRHQEGGAA--YPAPVDEFVLSCLDLSCGRTYSSEGPLRLGIVLEGSVRVNW 378

Query: 355 GSQQLQLKPGESAFI 369
            + Q++L  G+S  I
Sbjct: 379 ETGQMRLFRGQSFLI 393


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: 389
Number of extensions: 18
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: 416
Length adjustment: 31
Effective length of query: 360
Effective length of database: 385
Effective search space:   138600
Effective search space used:   138600
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_022947775.1 H035_RS18120 (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.20327.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.5e-77  247.1   0.0    1.9e-77  246.8   0.0    1.0  1  lcl|NCBI__GCF_000421465.1:WP_022947775.1  H035_RS18120 mannose-6-phosphate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000421465.1:WP_022947775.1  H035_RS18120 mannose-6-phosphate isomerase, class I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.8   0.0   1.9e-77   1.9e-77       7     356 ..      26     408 ..      24     411 .. 0.93

  Alignments for each domain:
  == domain 1  score: 246.8 bits;  conditional E-value: 1.9e-77
                                 TIGR00218   7 vqknlkerdWGkgtaladllgysipskq.taElWagaHkkgsSkvqng.kkvsLrdliekhksellGka 73 
                                               ++ ++++++WG+ ++++ llg ++p +   aElW gaH+  + +   g   vsL+dl+ +  + llG +
  lcl|NCBI__GCF_000421465.1:WP_022947775.1  26 LFCGVQQYAWGDFDFIPRLLGKTNPDRDpFAELWIGAHPDLPAQAVIGrTRVSLSDLLPEAVECLLGAD 94 
                                               67789********************9888***************999889******************* PP

                                 TIGR00218  74 eadrf..elPlLvkvLsaekplsiqvHPdkalakigyake..........krnYkDknhkpelvialtd 130
                                               ++ r+  +lP+L+k+L a +plsiqvHPdk+ a+ g+a+e          +rnY+D nhkpel+ altd
  lcl|NCBI__GCF_000421465.1:WP_022947775.1  95 AKIRYqgQLPFLMKILAAGRPLSIQVHPDKHQAEAGFAREhrlkipldspRRNYRDCNHKPELLCALTD 163
                                               *999999************************************************************** PP

                                 TIGR00218 131 fealkgfkp.......Lkriaelheeaer.....lgkteawviiasdekikeaaeilkealkns..... 182
                                               f+alkgf+p       L  i+e ++ aer     l+k    +++  +  + e  + ++ +l  +     
  lcl|NCBI__GCF_000421465.1:WP_022947775.1 164 FYALKGFRPeseiadqLASIPEWRGLAERfrdegLKKFYYHLMTLPQSVVDEMLAPVVARLRWEgpfpk 232
                                               *********999999999999999999998877788888888888888888888888888888899999 PP

                                 TIGR00218 183 .keelkekiqrliyp....edvglfkgllLnrvklkpgeaiyvrsgtvHAykggdvlEvmanSdnvvra 246
                                                ++e++ +    +y      d glf+  lLn + l+pgeai+ ++g++H y++g+ +EvmanS+nv+r 
  lcl|NCBI__GCF_000421465.1:WP_022947775.1 233 dRREYWLLRADELYSqgahHDRGLFSLYLLNFLCLRPGEAIFQHAGELHSYLEGVGVEVMANSNNVLRG 301
                                               999**99887666652222467*********************************************** PP

                                 TIGR00218 247 gltdkyldvkklvevltveekpeeklkeqkqkegaevlflvpieefavlktdlsekaelksqdsalill 315
                                               glt+k +dv+ l+e++++e k++e l +++q+ g    +++p++ef ++  dls   +  s+ +  + +
  lcl|NCBI__GCF_000421465.1:WP_022947775.1 302 GLTPKHVDVPALLEIVKFEGKKAEILSSRHQEGG--AAYPAPVDEFVLSCLDLSCGRTYSSEGPLRLGI 368
                                               ******************************9998..89*******************9*********** PP

                                 TIGR00218 316 vleGdglilsgekklklkkGesfliaakleevtiegedeal 356
                                               vleG+ ++  +  ++ l +G+sfli+       +++ed+ +
  lcl|NCBI__GCF_000421465.1:WP_022947775.1 369 VLEGSVRVNWETGQMRLFRGQSFLIPHGC-RCRLQSEDDVV 408
                                               **************************988.77777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (359 nodes)
Target sequences:                          1  (416 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: 8.67
//
[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