Alignments for a candidate for PS417_11890 in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_11890 in Dinoroseobacter shibae DFL-12

Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate 3607108 Dshi_0530 ABC transporter related (RefSeq)

Query= reanno::pseudo3_N2E3:AO353_21385
         (521 letters)



>FitnessBrowser__Dino:3607108
          Length = 498

 Score =  351 bits (901), Expect = e-101
 Identities = 184/481 (38%), Positives = 288/481 (59%)

Query: 28  LEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLR 87
           +++  ++K + GV AL  V   V+PG  + L GENG+GKSTL+KII+G+    AG +++ 
Sbjct: 10  IDLRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQIA 69

Query: 88  GKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCTAQ 147
           G+      P  +  AG+ +I Q+ +L P++S+AENI    +      +   R +      
Sbjct: 70  GQEHVTLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKFRAVRDIARA 129

Query: 148 LLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSII 207
            L+R+ + +D + +V  L +A++Q+V I +A++  + ++IMDEPT+A+T+KEV  L  II
Sbjct: 130 ALDRIGVQIDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQGII 189

Query: 208 ADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELSQ 267
             LK +G  +I+++HK+ EV  ++++V V R+G  +    A   D  SL   M GR++ +
Sbjct: 190 RMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTYHMTGRDVPE 249

Query: 268 LFPVREKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITP 327
           + P         LM V+ L   G F  +SFDL  GE+LGI GL+G GRT+VA+A+FG+  
Sbjct: 250 VPPSDVAAGAQTLMQVQGLGKAGSFSDISFDLRTGEVLGITGLLGCGRTSVAKALFGLVT 309

Query: 328 SDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNG 387
            D G I +DG PV + DP  A       + EDR   GLF   S+L N+ +  L  +   G
Sbjct: 310 PDAGSILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNVAVGRLDAHTSGG 369

Query: 388 FIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTR 447
           F+    L     D  ++L+VK P +E  + +LSGGNQQ+  LARWL   PR+LIL+ P+ 
Sbjct: 370 FLDMTGLAKEASDWLRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSRAPRVLILNGPSV 429

Query: 448 GIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQ 507
           G+DVG+KA+I+ +I  LA EG+ VI+IS +LPE+L    RV+VM EG ++  L+ +  T+
Sbjct: 430 GVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGRIIDALEGTALTE 489

Query: 508 E 508
           +
Sbjct: 490 D 490



 Score = 88.6 bits (218), Expect = 5e-22
 Identities = 68/247 (27%), Positives = 117/247 (47%), Gaps = 14/247 (5%)

Query: 17  PNAIPVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGI 76
           P   P D     + +   +G     + SD+   +R G VL + G  G G++++ K + G+
Sbjct: 248 PEVPPSDVAAGAQTLMQVQGLGKAGSFSDISFDLRTGEVLGITGLLGCGRTSVAKALFGL 307

Query: 77  YQPDAGELRLRGKPVTFDTPLAALQAGIAMIHQEL---NLMPHMSIAENIWIGR---EQL 130
             PDAG + + G PV    P AA  A I  + ++     L    SI  N+ +GR      
Sbjct: 308 VTPDAGSILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNVAVGRLDAHTS 367

Query: 131 NGFHMIDHREMHRCTAQLLERLRINL-DPEEQVGNLSIAERQMVEIAKAVSYDSDILIMD 189
            GF  +D   + +  +  L RL++   D E  V +LS   +Q V +A+ +S    +LI++
Sbjct: 368 GGF--LDMTGLAKEASDWLRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSRAPRVLILN 425

Query: 190 EPTSAITDKEVAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRAD 249
            P+  +     A +  II +L  +G G+I I+  + E+ +    V V R+G  I     D
Sbjct: 426 GPSVGVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGRII-----D 480

Query: 250 SMDGDSL 256
           +++G +L
Sbjct: 481 ALEGTAL 487



 Score = 85.9 bits (211), Expect = 3e-21
 Identities = 61/225 (27%), Positives = 111/225 (49%), Gaps = 5/225 (2%)

Query: 295 VSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFA 354
           V F +  GE + +AG  GSG++ + + I G+ P+  G + + GQ     +P ++   G  
Sbjct: 28  VDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQIAGQEHVTLNPRISAAAGVM 87

Query: 355 LLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQ 414
           ++ +D     LFP LSV EN+            F + +A+R +      ++ V+   L+ 
Sbjct: 88  VIFQD---FSLFPNLSVAENIAFTTQLSTRQRLF-KFRAVRDIARAALDRIGVQI-DLDA 142

Query: 415 CIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMI 474
            ++TL    +Q   + R L +  +++I+DEPT  +       +  +I  L  EG+AVI +
Sbjct: 143 RVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQGIIRMLKEEGVAVIFV 202

Query: 475 SSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGMSV 519
           S +L EVL +S++V+V+  G  +     SE   + +    +G  V
Sbjct: 203 SHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTYHMTGRDV 247


Lambda     K      H
   0.321    0.137    0.391 

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: 560
Number of extensions: 29
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 3
Length of query: 521
Length of database: 498
Length adjustment: 34
Effective length of query: 487
Effective length of database: 464
Effective search space:   225968
Effective search space used:   225968
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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Candidates (tab-delimited)
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