Alignments for a candidate for PS417_11890 in Rhizobium leguminosarum 3841

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_11890 in Rhizobium leguminosarum 3841

Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_011651404.1 RL_RS09075 sugar ABC transporter ATP-binding protein

Query= reanno::WCS417:GFF2332
         (517 letters)



>NCBI__GCF_000009265.1:WP_011651404.1
          Length = 492

 Score =  416 bits (1070), Expect = e-121
 Identities = 221/489 (45%), Positives = 313/489 (64%)

Query: 23  LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82
           LL++  + K F GV AL D +  +R G+V AL G NGAGKST +KI+ GI+  DAG IR 
Sbjct: 4   LLDVEGLKKSFGGVAALRDGRFELRAGSVHALCGGNGAGKSTFLKILMGIHNRDAGSIRR 63

Query: 83  RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTA 142
           RGK + F  P  A  +GIA+I QEL+ +PHM++AENI++GRE       ++ R M+R   
Sbjct: 64  RGKDVDFAGPADALASGIAIIEQELSPVPHMTVAENIYLGREPSTRFGGIDFRTMNRSAQ 123

Query: 143 ELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSI 202
            LL  L  ++   + + NLS+A+ Q+VEIAKA+S+D++++ MDEPTSAI EKE   LF+ 
Sbjct: 124 GLLDDLEFDIRATQYMMNLSVAQMQLVEIAKALSHDAEVIFMDEPTSAIGEKEAQQLFAA 183

Query: 203 IADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELS 262
           I  LK QG+GIVY++H+++E+F IAD   VFRDG Y+G      ++   LI M+VGREL+
Sbjct: 184 IRRLKGQGRGIVYVSHRLSEIFQIADSYTVFRDGAYVGSGDLKQISRPDLIRMIVGRELA 243

Query: 263 QLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGIT 322
           + +    TP  +  L V  L+     +D+SF    GEI GI GLMGSGRT +   +FG+ 
Sbjct: 244 EEYVKTNTPTSETGLEVTALSCPNKIEDISFSARKGEIFGIYGLMGSGRTEIFNCLFGLE 303

Query: 323 PSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGN 382
            SS G+I +DG  + +S P  A+  G AL+TEDRKL+GL    SV  N+ MA LP  + +
Sbjct: 304 KSSDGRIVVDGTRISVSKPADAMASGLALVTEDRKLTGLNLSDSVRANICMASLPEMSPS 363

Query: 383 GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPT 442
             + ++        +  + ++K       +  LSGGNQQK +L +W + NP++L+LDEPT
Sbjct: 364 FAMSRRREAEASRRIQAQFQIKAARDTMPVSGLSGGNQQKVVLGKWFLRNPKVLLLDEPT 423

Query: 443 RGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEAT 502
           RG+DVGAK EIYR+I   A+ G  V+MISSE+ EVLGMSDR+MVM  G+  G   R E  
Sbjct: 424 RGVDVGAKREIYRIICDFAAAGGTVVMISSEIDEVLGMSDRIMVMRAGKSAGIYSREETD 483

Query: 503 QEKVMQLAS 511
            + ++ L++
Sbjct: 484 AQSLVHLST 492



 Score = 75.5 bits (184), Expect = 4e-18
 Identities = 60/246 (24%), Positives = 117/246 (47%), Gaps = 15/246 (6%)

Query: 274 DLLLTVRDL--TLDGV--FKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQI 329
           +LLL V  L  +  GV   +D  F+L AG +  + G  G+G++   + + GI    +G I
Sbjct: 2   ELLLDVEGLKKSFGGVAALRDGRFELRAGSVHALCGGNGAGKSTFLKILMGIHNRDAGSI 61

Query: 330 TLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGF---IQ 386
              GK V  + P  A+  G A++  +++LS + P ++V EN+ +   P     G      
Sbjct: 62  RRRGKDVDFAGPADALASGIAII--EQELSPV-PHMTVAENIYLGREPSTRFGGIDFRTM 118

Query: 387 QKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGID 446
            ++ + L +D+   +R       Q +  LS    Q   +A+ L  +  ++ +DEPT  I 
Sbjct: 119 NRSAQGLLDDLEFDIRAT-----QYMMNLSVAQMQLVEIAKALSHDAEVIFMDEPTSAIG 173

Query: 447 VGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKV 506
                +++  I  L  +G  ++ +S  L E+  ++D   V  +G  +G+ D  + ++  +
Sbjct: 174 EKEAQQLFAAIRRLKGQGRGIVYVSHRLSEIFQIADSYTVFRDGAYVGSGDLKQISRPDL 233

Query: 507 MQLASG 512
           +++  G
Sbjct: 234 IRMIVG 239


Lambda     K      H
   0.320    0.136    0.381 

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: 539
Number of extensions: 17
Number of successful extensions: 4
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: 517
Length of database: 492
Length adjustment: 34
Effective length of query: 483
Effective length of database: 458
Effective search space:   221214
Effective search space used:   221214
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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