Alignments for a candidate for manP in Rhodococcus qingshengii djl-6-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for manP in Rhodococcus qingshengii djl-6-2

Align protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized)
to candidate WP_050655799.1 C1M55_RS13985 PTS transporter subunit EIIA

Query= BRENDA::O31645
         (650 letters)



>NCBI__GCF_002893965.1:WP_050655799.1
          Length = 689

 Score =  327 bits (839), Expect = 8e-94
 Identities = 198/502 (39%), Positives = 293/502 (58%), Gaps = 35/502 (6%)

Query: 3   LLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAIIIA 62
           ++A+T+CP GIAHTYMAA++L  A +R GV + VETQG  G    L    I  A A+I A
Sbjct: 198 IVAVTACPTGIAHTYMAADSLVAAGERAGVKVHVETQGSSG-STPLDPSVIAGAAAVIFA 256

Query: 63  ADRSVN-KDRFIGKKLLSVGVQDGIRKPEELIQKALNG-DIPVYRS-----ATKSESGNH 115
            D  V  ++RF GK +++ GV+  I +P++++ +AL   + P   +     A  ++S   
Sbjct: 257 TDVGVKGRERFAGKPVVASGVKRAINEPDKMLAEALRASENPAAATVDGTAAAAADSDAG 316

Query: 116 QEKKQNPIYRHLMNGVSFMVPFIVVGGLLIAVALTLGGEKTP---KGLVI-------PDD 165
                  + + L+ GVS+M+PF+  GGLLIA+   LGG +     K +V+       PD 
Sbjct: 317 SVGFGTHLRQVLLTGVSYMIPFVAAGGLLIALGFLLGGYEISGPAKDIVLNNSITNLPDG 376

Query: 166 SF----WKTIEQIGSASFSFMIPILAGYIAYSIADKPGLVPGMIGGYIAATGSFYDSASG 221
                    + QIGS +FSF++P LAGYIA++IAD+PG+ PG   G +A          G
Sbjct: 377 GLATYLGAVLFQIGSLAFSFLVPALAGYIAFAIADRPGIAPGFTAGAVAVF-------VG 429

Query: 222 AGFLGGIIAGFLAGYAALWIKKLKVPKAIQPIMPIIIIPVFASLIVGLAFVFLIGAPVAQ 281
           AGF+GG++ G +AG  AL+I ++ VP+ ++ +MP++IIP+FA+L+VG     ++G P+A 
Sbjct: 430 AGFIGGLVGGLIAGVVALYIGRIAVPQWLRGLMPVVIIPLFATLVVGALMFIVLGRPLAA 489

Query: 282 IFASLTVWLAGMKGSSSILLALILGAMISFDMGGPVNKVAFLFGSAMIG---EGNYEIMG 338
           I + LT WL G+ GSS+I L +ILG M+ FD+GGPVNK A+ F  A +         IM 
Sbjct: 490 ITSGLTDWLNGLSGSSAIFLGIILGLMMCFDLGGPVNKAAYAFAVAGLNVNDPATLRIMA 549

Query: 339 PIAVAICIPPIGLGIA-TFLGKRKFEASQREMGKAAFTMGLFGITEGAIPFAAQDPLRVI 397
            +  A  +PP+ + +A T L  + F  ++RE GKAA+ +G   I+EGAIPFAA DPLRVI
Sbjct: 550 AVMAAGMVPPLAMALASTVLRPKLFSEAERENGKAAWLLGSAFISEGAIPFAAADPLRVI 609

Query: 398 PSIMAGSMTGSVIAMIGNVGDRVAHGGPIVAVLGAVDHVLMFFIAVIAGSLVTALFVNVL 457
           PS+MAG      + M  +V     HGG  + V  AV  +  F +++ AG++V AL V   
Sbjct: 610 PSMMAGGAVTGALIMAFDVTLSAPHGG--IFVFFAVGGIGWFLVSLAAGTVVAALAVVGA 667

Query: 458 KKDITASPVLSETAPTSAPSEA 479
           K+     P  +E  P   P+ A
Sbjct: 668 KEFFRKGPSDAELDPEIVPAAA 689



 Score = 85.9 bits (211), Expect = 6e-21
 Identities = 54/147 (36%), Positives = 80/147 (54%), Gaps = 3/147 (2%)

Query: 504 DIISPELIEPNLS-GETSDDIIDELIQKLSRRGALLSESGFKQAILNREQQGTTAIGMNI 562
           +IISPELI  +   G T +D+I  L  +L+  G     +G   A L RE Q  T +   I
Sbjct: 13  EIISPELISLDTDLGSTKEDVIRSLAARLTAAGRASDAAGLVDAALAREAQSATGLPGGI 72

Query: 563 AIPHGKSEAVREPSVAFGIKRSGVDWNSLDGSEAKLIFMIAVPKESGGNQHLKILQMLSR 622
           AIPH ++EAV   S+ F      VD+ + DG  A L+F+IA P E  G +H+K+L  L+R
Sbjct: 73  AIPHCRAEAVSSASLGFARLDPKVDFGAPDG-PADLVFLIAAP-EGAGAEHMKLLSSLAR 130

Query: 623 KLMDDNYRERLLSVQTTEEAYKLLEEI 649
            L+   +   L    T +E  +L++E+
Sbjct: 131 ALVRPAFVTSLREASTPDEIVRLVDEV 157


Lambda     K      H
   0.319    0.137    0.386 

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: 1031
Number of extensions: 64
Number of successful extensions: 11
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 650
Length of database: 689
Length adjustment: 39
Effective length of query: 611
Effective length of database: 650
Effective search space:   397150
Effective search space used:   397150
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: 54 (25.4 bits)

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 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