Alignments for a candidate for manA in Tistlia consotensis USBA 355

GapMind for catabolism of small carbon sources

Alignments for a candidate for manA in Tistlia consotensis USBA 355

Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate WP_085124919.1 B9O00_RS22145 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase

Query= BRENDA::P07874
         (481 letters)



>NCBI__GCF_900177295.1:WP_085124919.1
          Length = 497

 Score =  471 bits (1213), Expect = e-137
 Identities = 242/472 (51%), Positives = 309/472 (65%), Gaps = 5/472 (1%)

Query: 3   PVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLA-FDGMQAPLLVCNKEHRF 61
           PV+LSGG+G+RLWPLSRK YPKQ  AL  D T+ Q+T+ R     G+  PL+VC++E RF
Sbjct: 26  PVLLSGGAGTRLWPLSRKHYPKQLQALLSDRTMLQETVLRTRDLAGVAPPLVVCHQEQRF 85

Query: 62  IVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVIEDQRAF 121
           +V EQL A  LA Q I+LEP GRNTAPA+ ++A+ L  E    LLL  PADH I D  AF
Sbjct: 86  LVTEQLAAVGLAPQRIVLEPSGRNTAPALVVSALLLAGEDPQGLLLAQPADHHIADPEAF 145

Query: 122 QQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEKPDEARA 181
           + A+A A  AA  G +V FG+  +RPETGYGYI+A A     EGV  V SFVEKP+ A A
Sbjct: 146 RAAVAQAARAARDGWLVTFGVRPTRPETGYGYIQAGAAIDGFEGVRAVLSFVEKPEAATA 205

Query: 182 REFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNIDAATFE 241
                + G YWNSG+FL     +L+E+++   D+   C  A+   + D +   +DA  FE
Sbjct: 206 ARLAGSPGCYWNSGVFLLPVGPFLDEVRRLQPDLLAACERAIAEGREDLEFFRLDAEAFE 265

Query: 242 CCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWD----VHAKDANGNVTKGDVLVH 297
             P   ID A+ME + R  VVP+  GW DVGSW  + +    +   +++GNV +GDV   
Sbjct: 266 SAPALPIDKAIMELSGRVAVVPVEMGWRDVGSWPVLHEALRTLRPTESDGNVFEGDVEAE 325

Query: 298 DSHNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQNH 357
              NC +  +G+LV+ +G+ED+ +V T DA+++A  D    V  +V+ L  + R E  +H
Sbjct: 326 SVRNCHIRADGRLVAALGVEDLTIVVTDDAVLVARTDEAARVGALVERLGRRNRQEVLHH 385

Query: 358 CEVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCDDKTF 417
             VYRPWGSY SVD G RFQVK I VKPGA LSLQMHHHRAEHWIVV GTA+V CD    
Sbjct: 386 STVYRPWGSYQSVDSGERFQVKRIVVKPGAELSLQMHHHRAEHWIVVRGTARVHCDGDER 445

Query: 418 LLTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGRT 469
           LL ENQSTYIP  + HRL+NPG +PL +IEVQSGSYLGEDDI R +D YGR+
Sbjct: 446 LLHENQSTYIPPGTTHRLSNPGILPLHLIEVQSGSYLGEDDIVRFQDSYGRS 497


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: 615
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: 497
Length adjustment: 34
Effective length of query: 447
Effective length of database: 463
Effective search space:   206961
Effective search space used:   206961
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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 2024 update 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