Alignments for a candidate for manA in Marinomonas arctica 328

GapMind for catabolism of small carbon sources

Alignments for a candidate for manA in Marinomonas arctica 328

Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate WP_111609056.1 DK187_RS19920 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase

Query= BRENDA::P07874
         (481 letters)



>NCBI__GCF_003259225.1:WP_111609056.1
          Length = 465

 Score =  496 bits (1277), Expect = e-145
 Identities = 244/468 (52%), Positives = 326/468 (69%), Gaps = 9/468 (1%)

Query: 3   PVILSGGSGSRLWPLSRKQYPKQFLALTGD-DTLFQQTIKRLAFDGMQAPLLVCNKEHRF 61
           PV+LSGG GSRLWPLSR+ +PKQ L LT    +L QQT+ R++   +Q P++VCN +HRF
Sbjct: 5   PVVLSGGVGSRLWPLSREHFPKQCLNLTDSLSSLLQQTLARMSHLNVQPPIVVCNDDHRF 64

Query: 62  IVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLV-AEGRDELLLILPADHVIEDQRA 120
           ++ +QL+   +    ++LEP GRNTAPAVA+AA +++ ++  D L+L+LPADHVI +  A
Sbjct: 65  LIAQQLQDMGVKGAKVMLEPVGRNTAPAVALAAFEVLQSDNEDSLMLVLPADHVIRNTAA 124

Query: 121 FQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEKPDEAR 180
           F++A+  A   A+ G +V FGI  +R ETGYGYI+A  DA        V+ FVEKPD A 
Sbjct: 125 FEKAIEQAKVLAKAGGLVTFGIKPTRAETGYGYIKAGQDAC-------VEKFVEKPDLAT 177

Query: 181 AREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNIDAATF 240
           A+ ++ +G Y WNSGMFLF+ S+YL ELK++  DIY     A      D D + I A  F
Sbjct: 178 AQSYLESGNYLWNSGMFLFQTSQYLAELKQYRPDIYAAVASAYGNRTEDLDFIRIGAEVF 237

Query: 241 ECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVLVHDSH 300
             CP  SIDYAVME T  A VVP +  W+D+G+W+++ D   KD+N NV  GDV+   + 
Sbjct: 238 TACPSESIDYAVMETTKNAKVVPYAGDWSDIGAWNALHDYSDKDSNHNVLVGDVMAESTT 297

Query: 301 NCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQNHCEV 360
           N L+    +LV+ +G+ ++VV+ET DA++I  KD+ QDVK +V  + A+GR E  +H  V
Sbjct: 298 NSLIRAESRLVATVGVNNLVVIETADAVLIMDKDQSQDVKKIVSRIKAEGRQEHMHHTTV 357

Query: 361 YRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCDDKTFLLT 420
           +RPWG+Y +VD+G R QVK I VKPG +LS+QMHHHRAEHW+VVSGTA+V   ++  LLT
Sbjct: 358 HRPWGTYQTVDLGDRHQVKRIMVKPGEKLSVQMHHHRAEHWVVVSGTAKVQNGEREILLT 417

Query: 421 ENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGR 468
           EN+STYIP+  VH L NPGKIPLE+IEVQSGSYLGEDDI R  D YGR
Sbjct: 418 ENESTYIPVGVVHALENPGKIPLELIEVQSGSYLGEDDIVRFSDRYGR 465


Lambda     K      H
   0.319    0.134    0.400 

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: 593
Number of extensions: 29
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: 481
Length of database: 465
Length adjustment: 33
Effective length of query: 448
Effective length of database: 432
Effective search space:   193536
Effective search space used:   193536
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
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