Alignments for a candidate for BPHYT_RS16930 in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for BPHYT_RS16930 in Dyella japonica UNC79MFTsu3.2

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein

Query= uniprot:B2SYR5
         (512 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2413
          Length = 505

 Score =  321 bits (823), Expect = 3e-92
 Identities = 189/495 (38%), Positives = 291/495 (58%), Gaps = 13/495 (2%)

Query: 5   LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64
           L+   +GK F    ALDGV   +  G+VH LMG+NGAGKSTL+K+L G  +PD G V +D
Sbjct: 13  LQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGSVELD 72

Query: 65  GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLP--NSLGWVNKREAKRFVR 122
           G  +  ++   +   GI  ++QE+   P+L+VAENL  G+ P    L  ++ R+ +   R
Sbjct: 73  GRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLYAGRYPRRRRLRMIDWRQVRDGAR 132

Query: 123 ERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKL 182
             L  + + LD +A L    +A RQMV I +AL  +ARV+ LDEPTSSL   E   LF++
Sbjct: 133 SLLRQLHLELDVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVRELFRV 192

Query: 183 VRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREI 242
           +  LR    A+++++H +D++Y + D  T+ RDG ++  +   + +    +V+ MVGR++
Sbjct: 193 IAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVAD-LPPAALVNAMVGRDL 251

Query: 243 SDIYNYSAR----PLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHL 298
             +    A     P       A+G+       P   +VRRGE++G  GL+G+GR+EL  L
Sbjct: 252 PTVAGADAERAPPPDAPPAIDAQGLGCRGKLHPVDLQVRRGEMLGLGGLLGSGRTELARL 311

Query: 299 VYGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRR 358
           ++G D  + GEL + G+ ++++   +A+  G+ LCPE+RK +GIVA  +V ENI ++ + 
Sbjct: 312 LFGLDRAERGELRIGGERVELKHPADAVVRGLALCPEERKTDGIVAELSVRENIVLALQA 371

Query: 359 HYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWL-AEPDLK 417
                GM   R ++ E A + ++ L IK       +  LSGGNQQK +L+RWL  EP  +
Sbjct: 372 RQGWRGM--SRARQDELARQLVQALGIKAADIETPVGLLSGGNQQKVMLARWLVTEP--R 427

Query: 418 VVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISG 477
           ++ILDEPTRGIDV AK E+   + + A  G A++ IS+E  E+    DRI VMR+ R +G
Sbjct: 428 LLILDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGELTRWCDRIAVMRERRKAG 487

Query: 478 ELTRKDATEQSVLSL 492
           EL    +TE  VL++
Sbjct: 488 ELP-GGSTEARVLAM 501



 Score = 87.0 bits (214), Expect = 1e-21
 Identities = 79/260 (30%), Positives = 123/260 (47%), Gaps = 18/260 (6%)

Query: 250 ARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGE 309
           AR LG+   A   ++G  LA      +R GE+    G  GAG+S L+ L+ G +    G 
Sbjct: 15  ARGLGKRFGATLALDGVDLA------LRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGS 68

Query: 310 LLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISC--RRHYLRVGMFL 367
           + LDG+ I   +  EA R GI    +   E  +    +V+EN+      RR  LR+  + 
Sbjct: 69  VELDGRVIAPSTPMEAQRDGIGTVYQ---EVNLCPNLSVAENLYAGRYPRRRRLRMIDWR 125

Query: 368 DRKKEAETADRFIKL-LKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTR 426
             +  A +  R + L L +  P     +       +Q   ++R L     +V+ILDEPT 
Sbjct: 126 QVRDGARSLLRQLHLELDVDAPLGSYPVAI-----RQMVAIARALGV-SARVLILDEPTS 179

Query: 427 GIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATE 486
            +D G   E++ VI QL ERG AI+ ++  L +V  VSDRI V+R G   GE    D   
Sbjct: 180 SLDEGEVRELFRVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPP 239

Query: 487 QSVLSLALPQSSTALPGTQA 506
            ++++  + +    + G  A
Sbjct: 240 AALVNAMVGRDLPTVAGADA 259


Lambda     K      H
   0.320    0.136    0.385 

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: 667
Number of extensions: 38
Number of successful extensions: 8
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: 512
Length of database: 505
Length adjustment: 34
Effective length of query: 478
Effective length of database: 471
Effective search space:   225138
Effective search space used:   225138
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 17 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