Alignments for a candidate for nupA in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for nupA in Dinoroseobacter shibae DFL-12

Align Purine/cytidine ABC transporter ATP-binding protein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement (characterized)
to candidate 3609459 Dshi_2843 ABC transporter related (RefSeq)

Query= TCDB::A2RKA7
         (506 letters)



>FitnessBrowser__Dino:3609459
          Length = 548

 Score =  453 bits (1165), Expect = e-132
 Identities = 240/501 (47%), Positives = 333/501 (66%), Gaps = 9/501 (1%)

Query: 7   IQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVK 66
           I++  ++K FG   AN  +++ +  G IH ++GENGAGKSTLM+IL G  +   GE+ +K
Sbjct: 26  IELRGISKAFGPVQANKDISIRVMPGTIHGIIGENGAGKSTLMSILYGFYKADAGEIFIK 85

Query: 67  GKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKILEL 126
           G+   I     A   GIGMV QHF LV+ FTV EN++LG E    +   L  A+K + EL
Sbjct: 86  GQKTEIPDSQAAIRAGIGMVFQHFKLVENFTVLENVVLGAEEGALLRPSLAKARKLLREL 145

Query: 127 SERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMK 186
           SE Y L+V PDALI D+SVG QQRVEILK LYR ADILI DEPT VLTPAE   L +I++
Sbjct: 146 SEEYELNVAPDALIEDLSVGHQQRVEILKALYRKADILILDEPTGVLTPAEADHLFRILE 205

Query: 187 NLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVSFI 246
            L  EGK+IILITHKL EI    D ++V+RRG+   TV+  D + ++LAELMVGR V   
Sbjct: 206 GLKAEGKTIILITHKLREIMETTDTVSVMRRGEMTATVKTADTSPEQLAELMVGRKVLLR 265

Query: 247 TEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAI- 305
            +K  AQP   +L + DL + + +G  +VKG+SL VRAGE++G+AG+ GNGQ+EL++ + 
Sbjct: 266 VDKTPAQPGAPILTVDDLRVVDDQGVERVKGISLQVRAGEVLGIAGVAGNGQSELLEVLG 325

Query: 306 -----TGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIAL 360
                TG   V    I L  K  +N + R+   Q + HVPEDR  +GL+++    EN+A 
Sbjct: 326 GMRPATGRVTVSGQQIDLTGKH-SNGKTRR--AQGIAHVPEDRQAEGLIMDYHAWENVAF 382

Query: 361 QTYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDR 420
             +  P  ++   +D   + + A   +  FDVR A  W++A + SGGNQQK ++AREI+R
Sbjct: 383 GYHDDPAYNRGLLMDNRAVRADAEGKIARFDVRPADCWLAAKNFSGGNQQKIVLAREIER 442

Query: 421 NPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQ 480
           NP+LL+V QPTRG+D+GAIE+IH+++I  RD GKA+L++S EL+EIL++SDR+AV+ DG+
Sbjct: 443 NPELLLVGQPTRGVDIGAIEFIHQQIIALRDAGKAILLVSVELEEILSLSDRVAVMFDGR 502

Query: 481 IQGIVSPETTTKQELGILMVG 501
           I G      T ++ELG+LM G
Sbjct: 503 IMGERPAAETNEKELGLLMAG 523



 Score = 86.7 bits (213), Expect = 2e-21
 Identities = 64/233 (27%), Positives = 115/233 (49%), Gaps = 16/233 (6%)

Query: 276 KGLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKLHNKDITNQRPRKITEQS 335
           K +S+ V  G I G+ G +G G++ L+  + G  K D+G I +  +       +      
Sbjct: 42  KDISIRVMPGTIHGIIGENGAGKSTLMSILYGFYKADAGEIFIKGQKTEIPDSQAAIRAG 101

Query: 336 VGHVPEDRHRDGLVLEMTVAENIALQT----YYKPPMSKYGFLDYNKINSHARELMEEFD 391
           +G V +      LV   TV EN+ L        +P ++K   L         REL EE++
Sbjct: 102 IGMVFQHFK---LVENFTVLENVVLGAEEGALLRPSLAKARKL--------LRELSEEYE 150

Query: 392 VRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARD 451
           +  A + +    LS G+QQ+  I + + R  D+LI+ +PT  L     +++ + L   + 
Sbjct: 151 LNVAPDAL-IEDLSVGHQQRVEILKALYRKADILILDEPTGVLTPAEADHLFRILEGLKA 209

Query: 452 EGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGILMVGGNI 504
           EGK +++I+ +L EI+  +D ++V+  G++   V    T+ ++L  LMVG  +
Sbjct: 210 EGKTIILITHKLREIMETTDTVSVMRRGEMTATVKTADTSPEQLAELMVGRKV 262


Lambda     K      H
   0.315    0.135    0.365 

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: 723
Number of extensions: 31
Number of successful extensions: 5
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: 506
Length of database: 548
Length adjustment: 35
Effective length of query: 471
Effective length of database: 513
Effective search space:   241623
Effective search space used:   241623
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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