Aligments for a candidate for bztC in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Aligments for a candidate for bztC in Dinoroseobacter shibae DFL-12

Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate 3606890 Dshi_0320 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= TCDB::Q52665
         (434 letters)



>lcl|FitnessBrowser__Dino:3606890 Dshi_0320 polar amino acid ABC
           transporter, inner membrane subunit (RefSeq)
          Length = 432

 Score =  455 bits (1170), Expect = e-132
 Identities = 230/440 (52%), Positives = 302/440 (68%), Gaps = 14/440 (3%)

Query: 1   MSDT----SFVRTEMLAPRPAPVSQVGAIKWMRENLFSGPLNTALTVFGLLATVWLVQAA 56
           MSDT    +FVRTE + P P PVS+VG + W+R NLF    ++ LT+       WL    
Sbjct: 1   MSDTHASAAFVRTEEIPPSPPPVSEVGIVNWLRSNLFYSIPSSILTLLTAAFIYWLSSIL 60

Query: 57  APWLLHGVWNANSLTECRAIIAERWGPEATGACWAVIRVRWNQFLFGFYPVDQYWRLFVT 116
            PW+ +GVW+ANS+ +CR I+       A G C+AVI  RW Q +FG YP ++YWR  + 
Sbjct: 61  MPWMFNGVWDANSIRDCREIL-----DGAIGGCFAVIAERWPQLIFGNYPNEEYWRAVLA 115

Query: 117 FAGLFLALAPVLFDALPRKLIWGTLLYPLAAFWLLWGGPIWGPVSVLAGFAILGLLFTAL 176
           F GLF+ALAPVLF  LPRK++W T L+P  A+WL+WGG  W  V  L G  +  + F AL
Sbjct: 116 FVGLFVALAPVLFFKLPRKMLWFTGLFPFIAYWLIWGGSAWVSVMALVGVVVGYVAFKAL 175

Query: 177 APK--LGVPVSAGIGLVVAALFWLYAAAPIEAALQSALPLALPEVDSDQFGGFLLALVIG 234
             +   G  V+A   L    LFW++ +     AL S + L+LP+V+S   GGF++  ++G
Sbjct: 176 EERSFFGAIVAA---LFATLLFWIFISPLAVNALSSVVALSLPQVESRFIGGFMINFILG 232

Query: 235 VTAIVVSLPLGILLALGRQSDMLIVKSLSVGIIEFVRGVPLITLLFTASLLLQYFLPPGT 294
            + I +SLPLGI LALGRQS++ I+K + V  IEF+RGVPLITLLF AS++L YFLPPGT
Sbjct: 233 TSGIALSLPLGIALALGRQSNLPIIKGVCVVFIEFIRGVPLITLLFVASVMLAYFLPPGT 292

Query: 295 NFDLILRVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYWQAQRLIIMPQALK 354
           +FDL+LRV+I++TLFA+AYIAE IRGGLAALPRGQYEA D+LGLDYWQ+ RLII+PQALK
Sbjct: 293 SFDLVLRVIIMITLFASAYIAEAIRGGLAALPRGQYEAGDSLGLDYWQSMRLIILPQALK 352

Query: 355 ISIPGIVSSFIGLFKDTTLVAFVGLFDPLKGISNVVRSDMAWKGTYWEPYIFVALIFFLF 414
           ISIP IV+  IGLFKDTTLV+ + +FD L  I   + S   W G YWE   F  ++FF+F
Sbjct: 353 ISIPSIVNIAIGLFKDTTLVSIISMFDMLGMIQGPILSSTEWFGVYWELLGFAGVLFFVF 412

Query: 415 NFSMSRYSMYLERKLKRDHR 434
            + +S+YS +LER+L  +HR
Sbjct: 413 CYGISQYSQWLERQLATEHR 432


Lambda     K      H
   0.329    0.143    0.457 

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: 37
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 434
Length of database: 432
Length adjustment: 32
Effective length of query: 402
Effective length of database: 400
Effective search space:   160800
Effective search space used:   160800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 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 preprint on GapMind for carbon sources, or view the source code.

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